13-26431441-G-C

Variant names:

• chr13-26431441-G-C
• rs513093

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 0.658 in 152,116 control chromosomes in the GnomAD database, including 33,182 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 0.66 (33182 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.71
• Publications: 3 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 (AFR) allele frequency at 95% confidence interval = 0.721 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: 0.658 AC: 100074 AN: 151998 Hom.: 33169 Cov.: 32

Gnomad AFR AF: 0.728

Gnomad AMI AF: 0.611

Gnomad AMR AF: 0.615

Gnomad ASJ AF: 0.701

Gnomad EAS AF: 0.435

Gnomad SAS AF: 0.636

Gnomad FIN AF: 0.714

Gnomad MID AF: 0.668

Gnomad NFE AF: 0.634

Gnomad OTH AF: 0.650

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

GnomAD4 genome AF: 0.658 AC: 100127 AN: 152116 Hom.: 33182 Cov.: 32 AF XY: 0.662 AC XY: 49203 AN XY: 74348

African (AFR) AF: 0.728 AC: 30229 AN: 41506

American (AMR) AF: 0.614 AC: 9376 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.701 AC: 2434 AN: 3470

East Asian (EAS) AF: 0.435 AC: 2245 AN: 5164

South Asian (SAS) AF: 0.635 AC: 3059 AN: 4820

European-Finnish (FIN) AF: 0.714 AC: 7558 AN: 10592

Middle Eastern (MID) AF: 0.663 AC: 195 AN: 294

European-Non Finnish (NFE) AF: 0.634 AC: 43105 AN: 67966

Other (OTH) AF: 0.648 AC: 1369 AN: 2112

Alfa AF: 0.551 Hom.: 1559

Bravo AF: 0.647

Asia WGS AF: 0.577 AC: 2010 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.14
DANN	Benign	0.36
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs513093; hg19: chr13-27005578;