rs13272289

Variant names:

• chr8-6261109-G-A
• rs13272289

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 0.404 in 151,784 control chromosomes in the GnomAD database, including 13,553 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 0.40 (13553 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.03
• Publications: 2 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 (EAS) allele frequency at 95% confidence interval = 0.634 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: 0.404 AC: 61260 AN: 151666 Hom.: 13539 Cov.: 29

Gnomad AFR AF: 0.228

Gnomad AMI AF: 0.646

Gnomad AMR AF: 0.552

Gnomad ASJ AF: 0.497

Gnomad EAS AF: 0.653

Gnomad SAS AF: 0.416

Gnomad FIN AF: 0.517

Gnomad MID AF: 0.383

Gnomad NFE AF: 0.432

Gnomad OTH AF: 0.408

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

GnomAD4 genome AF: 0.404 AC: 61291 AN: 151784 Hom.: 13553 Cov.: 29 AF XY: 0.411 AC XY: 30489 AN XY: 74152

African (AFR) AF: 0.228 AC: 9442 AN: 41404

American (AMR) AF: 0.553 AC: 8425 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.497 AC: 1725 AN: 3470

East Asian (EAS) AF: 0.653 AC: 3344 AN: 5124

South Asian (SAS) AF: 0.416 AC: 2002 AN: 4808

European-Finnish (FIN) AF: 0.517 AC: 5420 AN: 10488

Middle Eastern (MID) AF: 0.391 AC: 115 AN: 294

European-Non Finnish (NFE) AF: 0.432 AC: 29367 AN: 67942

Other (OTH) AF: 0.411 AC: 866 AN: 2106

Alfa AF: 0.376 Hom.: 5984

Bravo AF: 0.404

Asia WGS AF: 0.518 AC: 1798 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.59
DANN	Benign	0.88
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs13272289; hg19: chr8-6118630;