chr13-26708547-G-A

Variant names:

• chr13-26708547-G-A
• rs4771006

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 0.417 in 146,186 control chromosomes in the GnomAD database, including 13,106 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 0.42 (13106 hom., cov: 28)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.26
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.479 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.417 AC: 60973 AN: 146070 Hom.: 13098 Cov.: 28

Gnomad AFR AF: 0.272

Gnomad AMI AF: 0.333

Gnomad AMR AF: 0.428

Gnomad ASJ AF: 0.374

Gnomad EAS AF: 0.472

Gnomad SAS AF: 0.422

Gnomad FIN AF: 0.505

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.483

Gnomad OTH AF: 0.447

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

GnomAD4 genome AF: 0.417 AC: 61001 AN: 146186 Hom.: 13106 Cov.: 28 AF XY: 0.420 AC XY: 29822 AN XY: 71076

African (AFR) AF: 0.272 AC: 10496 AN: 38568

American (AMR) AF: 0.427 AC: 6291 AN: 14726

Ashkenazi Jewish (ASJ) AF: 0.374 AC: 1277 AN: 3412

East Asian (EAS) AF: 0.472 AC: 2391 AN: 5062

South Asian (SAS) AF: 0.421 AC: 1880 AN: 4466

European-Finnish (FIN) AF: 0.505 AC: 5051 AN: 9996

Middle Eastern (MID) AF: 0.503 AC: 146 AN: 290

European-Non Finnish (NFE) AF: 0.483 AC: 32255 AN: 66756

Other (OTH) AF: 0.454 AC: 919 AN: 2024

Alfa AF: 0.446 Hom.: 20371

Bravo AF: 0.390

Asia WGS AF: 0.440 AC: 1529 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.60
DANN	Benign	0.60
PhyloP100		-2.3

Splicing

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

Other links and lift over

dbSNP: rs4771006; hg19: chr13-27282684; COSMIC: COSV53406226;