13-103864501-C-T

Variant names:

• chr13-103864501-C-T
• rs7336950

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 0.128 in 152,088 control chromosomes in the GnomAD database, including 1,479 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 (1479 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.176
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.244 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.128 AC: 19418 AN: 151970 Hom.: 1472 Cov.: 32

Gnomad AFR AF: 0.168

Gnomad AMI AF: 0.127

Gnomad AMR AF: 0.178

Gnomad ASJ AF: 0.0363

Gnomad EAS AF: 0.255

Gnomad SAS AF: 0.188

Gnomad FIN AF: 0.0595

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.0936

Gnomad OTH AF: 0.124

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

GnomAD4 genome AF: 0.128 AC: 19440 AN: 152088 Hom.: 1479 Cov.: 32 AF XY: 0.129 AC XY: 9574 AN XY: 74336

African (AFR) AF: 0.168 AC: 6961 AN: 41480

American (AMR) AF: 0.179 AC: 2728 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.0363 AC: 126 AN: 3468

East Asian (EAS) AF: 0.256 AC: 1319 AN: 5156

South Asian (SAS) AF: 0.187 AC: 902 AN: 4812

European-Finnish (FIN) AF: 0.0595 AC: 630 AN: 10586

Middle Eastern (MID) AF: 0.109 AC: 32 AN: 294

European-Non Finnish (NFE) AF: 0.0936 AC: 6366 AN: 67994

Other (OTH) AF: 0.123 AC: 260 AN: 2116

Alfa AF: 0.108 Hom.: 3071

Bravo AF: 0.138

Asia WGS AF: 0.223 AC: 774 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.2
DANN	Benign	0.73
PhyloP100		-0.18

Splicing

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

Other links and lift over

dbSNP: rs7336950; hg19: chr13-104516851;