dbSNP rs2887286: SDF4:c.557-1824A>G (chr1-1220751-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000360001.12(SDF4):c.557-1824A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.229 in 1,288,494 control chromosomes in the GnomAD database, including 46,944 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.31 ( 10080 hom., cov: 34)

Exomes 𝑓: 0.22 ( 36864 hom. )

Consequence

SDF4
ENST00000360001.12 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0470

Publications

17 publications found

Variant links:

Genes affected

SDF4 (HGNC:24188): (stromal cell derived factor 4) This gene encodes a stromal cell derived factor that is a member of the CREC protein family. The encoded protein contains six EF-hand motifs and calcium-binding motifs. This protein localizes to the Golgi lumen and may be involved in regulating calcium dependent cellular activities. [provided by RefSeq, Sep 2011]

SDF4 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.9).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.814 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000360001.12. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SDF4	NM_016176.6	MANE Select	c.557-1824A>G		intron	N/A	NP_057260.3
	SDF4	NM_016547.3		c.557-1824A>G		intron	N/A	NP_057631.2

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
SDF4	ENST00000360001.12	TSL:1 MANE Select	c.557-1824A>G	intron	N/A	ENSP00000353094.7
SDF4	ENST00000263741.12	TSL:1	c.557-1824A>G	intron	N/A	ENSP00000263741.8
SDF4	ENST00000494748.1	TSL:2	n.601A>G	non_coding_transcript_exon	Exon 1 of 3

Frequencies

GnomAD3 genomes

AF:

0.313

AC:

47478

AN:

151878

Hom.:

10048

Cov.:

show subpopulations

Gnomad AFR

AF:

0.482

Gnomad AMI

AF:

0.142

Gnomad AMR

AF:

0.431

Gnomad ASJ

AF:

0.164

Gnomad EAS

AF:

0.836

Gnomad SAS

AF:

0.529

Gnomad FIN

AF:

0.171

Gnomad MID

AF:

0.165

Gnomad NFE

AF:

0.161

Gnomad OTH

AF:

0.300

GnomAD2 exomes

AF:

0.368

AC:

47149

AN:

128100

AF XY:

0.366

show subpopulations

Gnomad AFR exome

AF:

0.486

Gnomad AMR exome

AF:

0.539

Gnomad ASJ exome

AF:

0.162

Gnomad EAS exome

AF:

0.844

Gnomad FIN exome

AF:

0.171

Gnomad NFE exome

AF:

0.161

Gnomad OTH exome

AF:

0.276

GnomAD4 exome

AF:

0.217

AC:

246972

AN:

1136498

Hom.:

36864

Cov.:

AF XY:

0.226

AC XY:

125990

AN XY:

557538

show subpopulations

African (AFR)

AF:

0.479

AC:

11683

AN:

24396

American (AMR)

AF:

0.535

AC:

15130

AN:

28256

Ashkenazi Jewish (ASJ)

AF:

0.161

AC:

2572

AN:

15934

East Asian (EAS)

AF:

0.839

AC:

10777

AN:

12838

South Asian (SAS)

AF:

0.500

AC:

38079

AN:

76182

European-Finnish (FIN)

AF:

0.175

AC:

2220

AN:

12650

Middle Eastern (MID)

AF:

0.204

AC:

895

AN:

4392

European-Non Finnish (NFE)

AF:

0.168

AC:

154726

AN:

920344

Other (OTH)

AF:

0.262

AC:

10890

AN:

41506

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.467

Heterozygous variant carriers

8847

17694

26540

35387

44234

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

6878

13756

20634

27512

34390

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.313

AC:

47559

AN:

151996

Hom.:

10080

Cov.:

AF XY:

0.321

AC XY:

23823

AN XY:

74304

show subpopulations

African (AFR)

AF:

0.482

AC:

19964

AN:

41438

American (AMR)

AF:

0.432

AC:

6601

AN:

15282

Ashkenazi Jewish (ASJ)

AF:

0.164

AC:

568

AN:

3466

East Asian (EAS)

AF:

0.835

AC:

4319

AN:

5172

South Asian (SAS)

AF:

0.528

AC:

2548

AN:

4822

European-Finnish (FIN)

AF:

0.171

AC:

1803

AN:

10554

Middle Eastern (MID)

AF:

0.160

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.161

AC:

10932

AN:

67948

Other (OTH)

AF:

0.307

AC:

648

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

1478

2955

4433

5910

7388

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

450

900

1350

1800

2250

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.211

Hom.:

9179

Bravo

AF:

0.336

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

1.8

(source)

DANN

Benign

0.57

PhyloP100

0.047

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.050

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over