13-105404308-A-T

Variant names:

• chr13-105404308-A-T
• rs2181953

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 0.629 in 151,830 control chromosomes in the GnomAD database, including 31,523 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 0.63 (31523 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00700
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.827 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: 0.628 AC: 95317 AN: 151710 Hom.: 31459 Cov.: 31

Gnomad AFR AF: 0.834

Gnomad AMI AF: 0.388

Gnomad AMR AF: 0.624

Gnomad ASJ AF: 0.453

Gnomad EAS AF: 0.713

Gnomad SAS AF: 0.538

Gnomad FIN AF: 0.627

Gnomad MID AF: 0.557

Gnomad NFE AF: 0.518

Gnomad OTH AF: 0.590

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

GnomAD4 genome AF: 0.629 AC: 95445 AN: 151830 Hom.: 31523 Cov.: 31 AF XY: 0.632 AC XY: 46879 AN XY: 74182

African (AFR) AF: 0.834 AC: 34572 AN: 41460

American (AMR) AF: 0.624 AC: 9492 AN: 15210

Ashkenazi Jewish (ASJ) AF: 0.453 AC: 1574 AN: 3472

East Asian (EAS) AF: 0.713 AC: 3665 AN: 5142

South Asian (SAS) AF: 0.539 AC: 2591 AN: 4810

European-Finnish (FIN) AF: 0.627 AC: 6607 AN: 10530

Middle Eastern (MID) AF: 0.554 AC: 163 AN: 294

European-Non Finnish (NFE) AF: 0.518 AC: 35189 AN: 67906

Other (OTH) AF: 0.591 AC: 1240 AN: 2098

Alfa AF: 0.585 Hom.: 3173

Bravo AF: 0.638

Asia WGS AF: 0.635 AC: 2206 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	2.5
DANN	Benign	0.34
PhyloP100		-0.0070

Splicing

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

Other links and lift over

dbSNP: rs2181953; hg19: chr13-106056658;