rs13272289

Positions:

• chr8-6261109-G-A

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.228

Gnomad4 AMR AF: 0.553

Gnomad4 ASJ AF: 0.497

Gnomad4 EAS AF: 0.653

Gnomad4 SAS AF: 0.416

Gnomad4 FIN AF: 0.517

Gnomad4 NFE AF: 0.432

Gnomad4 OTH AF: 0.411

Alfa AF: 0.404 Hom.: 3300

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13272289; hg19: chr8-6118630;