13-105445901-T-C

Variant names:

• chr13-105445901-T-C
• rs9301029

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 0.649 in 152,058 control chromosomes in the GnomAD database, including 32,771 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 0.65 (32771 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.219
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.756 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: 0.649 AC: 98630 AN: 151940 Hom.: 32757 Cov.: 32

Gnomad AFR AF: 0.486

Gnomad AMI AF: 0.663

Gnomad AMR AF: 0.741

Gnomad ASJ AF: 0.651

Gnomad EAS AF: 0.776

Gnomad SAS AF: 0.648

Gnomad FIN AF: 0.657

Gnomad MID AF: 0.677

Gnomad NFE AF: 0.715

Gnomad OTH AF: 0.675

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

GnomAD4 genome AF: 0.649 AC: 98682 AN: 152058 Hom.: 32771 Cov.: 32 AF XY: 0.648 AC XY: 48138 AN XY: 74302

African (AFR) AF: 0.486 AC: 20150 AN: 41458

American (AMR) AF: 0.742 AC: 11338 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.651 AC: 2259 AN: 3470

East Asian (EAS) AF: 0.777 AC: 4004 AN: 5156

South Asian (SAS) AF: 0.648 AC: 3123 AN: 4822

European-Finnish (FIN) AF: 0.657 AC: 6937 AN: 10560

Middle Eastern (MID) AF: 0.673 AC: 198 AN: 294

European-Non Finnish (NFE) AF: 0.715 AC: 48635 AN: 67986

Other (OTH) AF: 0.679 AC: 1435 AN: 2112

Alfa AF: 0.687 Hom.: 23500

Bravo AF: 0.652

Asia WGS AF: 0.700 AC: 2432 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.3
DANN	Benign	0.22
PhyloP100		-0.22

Splicing

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

Other links and lift over

dbSNP: rs9301029; hg19: chr13-106098250;