13-103751248-C-T

Variant names:

• chr13-103751248-C-T
• rs1018685

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.856 in 151,660 control chromosomes in the GnomAD database, including 56,087 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 0.86 (56087 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0190
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.92 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.856 AC: 129693 AN: 151544 Hom.: 56046 Cov.: 32

Gnomad AFR AF: 0.781

Gnomad AMI AF: 0.932

Gnomad AMR AF: 0.765

Gnomad ASJ AF: 0.872

Gnomad EAS AF: 0.663

Gnomad SAS AF: 0.828

Gnomad FIN AF: 0.920

Gnomad MID AF: 0.915

Gnomad NFE AF: 0.926

Gnomad OTH AF: 0.855

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

GnomAD4 genome AF: 0.856 AC: 129791 AN: 151660 Hom.: 56087 Cov.: 32 AF XY: 0.852 AC XY: 63139 AN XY: 74106

African (AFR) AF: 0.782 AC: 32374 AN: 41424

American (AMR) AF: 0.765 AC: 11599 AN: 15168

Ashkenazi Jewish (ASJ) AF: 0.872 AC: 3022 AN: 3464

East Asian (EAS) AF: 0.663 AC: 3393 AN: 5116

South Asian (SAS) AF: 0.828 AC: 3991 AN: 4818

European-Finnish (FIN) AF: 0.920 AC: 9747 AN: 10600

Middle Eastern (MID) AF: 0.905 AC: 266 AN: 294

European-Non Finnish (NFE) AF: 0.926 AC: 62742 AN: 67756

Other (OTH) AF: 0.857 AC: 1807 AN: 2108

Alfa AF: 0.861 Hom.: 18564

Bravo AF: 0.838

Asia WGS AF: 0.727 AC: 2528 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.9
DANN	Benign	0.29
PhyloP100		0.019

Splicing

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

Other links and lift over

dbSNP: rs1018685; hg19: chr13-104403598;