chr13-105509652-T-C

Variant names:

• chr13-105509652-T-C
• rs3916971

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 0.472 in 152,118 control chromosomes in the GnomAD database, including 18,726 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 0.47 (18726 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0440
• Publications: 12 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.61).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.582 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: 0.472 AC: 71715 AN: 152000 Hom.: 18713 Cov.: 33

Gnomad AFR AF: 0.237

Gnomad AMI AF: 0.743

Gnomad AMR AF: 0.591

Gnomad ASJ AF: 0.518

Gnomad EAS AF: 0.462

Gnomad SAS AF: 0.514

Gnomad FIN AF: 0.536

Gnomad MID AF: 0.585

Gnomad NFE AF: 0.569

Gnomad OTH AF: 0.475

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

GnomAD4 genome AF: 0.472 AC: 71747 AN: 152118 Hom.: 18726 Cov.: 33 AF XY: 0.475 AC XY: 35290 AN XY: 74352

African (AFR) AF: 0.237 AC: 9827 AN: 41504

American (AMR) AF: 0.592 AC: 9049 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.518 AC: 1798 AN: 3470

East Asian (EAS) AF: 0.462 AC: 2391 AN: 5170

South Asian (SAS) AF: 0.515 AC: 2481 AN: 4822

European-Finnish (FIN) AF: 0.536 AC: 5668 AN: 10580

Middle Eastern (MID) AF: 0.595 AC: 175 AN: 294

European-Non Finnish (NFE) AF: 0.569 AC: 38691 AN: 67974

Other (OTH) AF: 0.469 AC: 991 AN: 2114

Alfa AF: 0.539 Hom.: 59416

Bravo AF: 0.464

Asia WGS AF: 0.449 AC: 1561 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.61
CADD	Benign	8.2
DANN	Benign	0.90
PhyloP100		0.044

Splicing

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

Other links and lift over

dbSNP: rs3916971; hg19: chr13-106162001;