dbSNP rs1859441: LOC105369750:n.227-321C>T (chr12-48029450-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The XR_001749115.3(LOC105369750):n.227-321C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.208 in 152,234 control chromosomes in the GnomAD database, including 3,781 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 0.21 ( 3781 hom., cov: 33)

Consequence

LOC105369750
XR_001749115.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.725

Publications

8 publications found

Variant links:

Genes affected

LOC105369750 (HGNC:):

LOC105369750 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=-0.93).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.438 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
LOC105369750	XR_001749115.3 link	n.227-321C>T	intron_variant	Intron 2 of 2
LOC105369750	XR_001749116.3 link	n.168-321C>T	intron_variant	Intron 2 of 2
LOC105369750	XR_944904.3 link	n.227-321C>T	intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes

AF:

0.208

AC:

31584

AN:

152118

Hom.:

3775

Cov.:

show subpopulations

Gnomad AFR

AF:

0.198

Gnomad AMI

AF:

0.243

Gnomad AMR

AF:

0.322

Gnomad ASJ

AF:

0.194

Gnomad EAS

AF:

0.453

Gnomad SAS

AF:

0.302

Gnomad FIN

AF:

0.235

Gnomad MID

AF:

0.139

Gnomad NFE

AF:

0.159

Gnomad OTH

AF:

0.203

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.208

AC:

31620

AN:

152234

Hom.:

3781

Cov.:

AF XY:

0.215

AC XY:

16019

AN XY:

74412

show subpopulations

African (AFR)

AF:

0.197

AC:

8200

AN:

41532

American (AMR)

AF:

0.323

AC:

4936

AN:

15300

Ashkenazi Jewish (ASJ)

AF:

0.194

AC:

672

AN:

3470

East Asian (EAS)

AF:

0.453

AC:

2347

AN:

5182

South Asian (SAS)

AF:

0.302

AC:

1457

AN:

4826

European-Finnish (FIN)

AF:

0.235

AC:

2487

AN:

10602

Middle Eastern (MID)

AF:

0.137

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.159

AC:

10818

AN:

68002

Other (OTH)

AF:

0.208

AC:

441

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1275

2550

3825

5100

6375

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

336

672

1008

1344

1680

<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:

0.180

Hom.:

5625

Bravo

AF:

0.217

Asia WGS

AF:

0.375

AC:

1301

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.93

CADD

Benign

0.36

(source)

DANN

Benign

0.59

PhyloP100

-0.72

Splicing

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

ClinVar

Computational scores

Splicing

Publications

Other links and lift over