dbSNP rs11721: SDF4:c.*261G>T (chr1-1217251-C-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_016176.6(SDF4):c.*261G>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.125 in 182,308 control chromosomes in the GnomAD database, including 1,887 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 0.13 ( 1654 hom., cov: 33)

Exomes 𝑓: 0.10 ( 233 hom. )

Consequence

SDF4
NM_016176.6 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.461

Publications

23 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=-0.94).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.238 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
SDF4	NM_016176.6 link	c.*261G>T	3_prime_UTR_variant	Exon 7 of 7	ENST00000360001.12	NP_057260.3
SDF4	NM_016547.3 link	c.*419G>T	3_prime_UTR_variant	Exon 7 of 7		NP_057631.2	Q9BRK5A0A024R0A9
SDF4	XM_047422111.1 link	c.*261G>T	3_prime_UTR_variant	Exon 7 of 7		XP_047278067.1
SDF4	XM_047422112.1 link	c.*419G>T	3_prime_UTR_variant	Exon 7 of 7		XP_047278068.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SDF4	ENST00000360001.12 link	c.*261G>T		3_prime_UTR_variant	Exon 7 of 7	1	NM_016176.6	ENSP00000353094.7		A0A5F9UP49

Frequencies

GnomAD3 genomes

AF:

0.130

AC:

19710

AN:

151990

Hom.:

1635

Cov.:

show subpopulations

Gnomad AFR

AF:

0.224

Gnomad AMI

AF:

0.0932

Gnomad AMR

AF:

0.0672

Gnomad ASJ

AF:

0.0545

Gnomad EAS

AF:

0.249

Gnomad SAS

AF:

0.0847

Gnomad FIN

AF:

0.125

Gnomad MID

AF:

0.0665

Gnomad NFE

AF:

0.0860

Gnomad OTH

AF:

0.121

GnomAD4 exome

AF:

0.102

AC:

3081

AN:

30200

Hom.:

233

Cov.:

AF XY:

0.0997

AC XY:

1588

AN XY:

15922

show subpopulations

African (AFR)

AF:

0.214

AC:

120

AN:

562

American (AMR)

AF:

0.0750

AC:

AN:

720

Ashkenazi Jewish (ASJ)

AF:

0.0372

AC:

AN:

780

East Asian (EAS)

AF:

0.257

AC:

557

AN:

2168

South Asian (SAS)

AF:

0.0692

AC:

AN:

260

European-Finnish (FIN)

AF:

0.131

AC:

595

AN:

4554

Middle Eastern (MID)

AF:

0.0373

AC:

AN:

134

European-Non Finnish (NFE)

AF:

0.0795

AC:

1535

AN:

19320

Other (OTH)

AF:

0.0987

AC:

168

AN:

1702

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

124

248

372

496

620

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

100

<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:

0.130

AC:

19755

AN:

152108

Hom.:

1654

Cov.:

AF XY:

0.131

AC XY:

9765

AN XY:

74358

show subpopulations

African (AFR)

AF:

0.225

AC:

9329

AN:

41506

American (AMR)

AF:

0.0670

AC:

1025

AN:

15298

Ashkenazi Jewish (ASJ)

AF:

0.0545

AC:

189

AN:

3470

East Asian (EAS)

AF:

0.250

AC:

1287

AN:

5154

South Asian (SAS)

AF:

0.0844

AC:

407

AN:

4822

European-Finnish (FIN)

AF:

0.125

AC:

1319

AN:

10586

Middle Eastern (MID)

AF:

0.0714

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0859

AC:

5840

AN:

67962

Other (OTH)

AF:

0.120

AC:

253

AN:

2104

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

828

1657

2485

3314

4142

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

210

420

630

840

1050

<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:

0.104

Hom.:

733

Bravo

AF:

0.132

Asia WGS

AF:

0.173

AC:

601

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.94

CADD

Benign

0.89

(source)

DANN

Benign

0.69

PhyloP100

-0.46

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over