rs9271858

Variant names:

• chr6-32627446-A-G
• rs9271858

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BP4_Strong BS2

The variant allele was found at a frequency of 0.445 in 130,172 control chromosomes in the GnomAD database, including 13,784 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 0.45 (13784 hom., cov: 24)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0110
• Publications: 31 publications found

ACMG classification

Our verdict: Benign. The variant received -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BS2: High Homozygotes in GnomAd4 at 13784 gene

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: 0.445 AC: 57891 AN: 130066 Hom.: 13777 Cov.: 24

Gnomad AFR AF: 0.413

Gnomad AMI AF: 0.450

Gnomad AMR AF: 0.425

Gnomad ASJ AF: 0.557

Gnomad EAS AF: 0.326

Gnomad SAS AF: 0.386

Gnomad FIN AF: 0.451

Gnomad MID AF: 0.595

Gnomad NFE AF: 0.473

Gnomad OTH AF: 0.492

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

GnomAD4 genome AF: 0.445 AC: 57935 AN: 130172 Hom.: 13784 Cov.: 24 AF XY: 0.441 AC XY: 27961 AN XY: 63458

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.414 AC: 14600 AN: 35294

American (AMR) AF: 0.424 AC: 5406 AN: 12744

Ashkenazi Jewish (ASJ) AF: 0.557 AC: 1689 AN: 3034

East Asian (EAS) AF: 0.325 AC: 1525 AN: 4696

South Asian (SAS) AF: 0.388 AC: 1526 AN: 3936

European-Finnish (FIN) AF: 0.451 AC: 3937 AN: 8736

Middle Eastern (MID) AF: 0.592 AC: 141 AN: 238

European-Non Finnish (NFE) AF: 0.473 AC: 27877 AN: 58910

Other (OTH) AF: 0.490 AC: 875 AN: 1786

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0.000000), which strongly suggests a high chance of mosaicism in these individuals.

Alfa AF: 0.489 Hom.: 35006

Bravo AF: 0.479

Asia WGS AF: 0.398 AC: 1385 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	5.7
DANN	Benign	0.46
PhyloP100		0.011

Splicing

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

Other links and lift over

dbSNP: rs9271858; hg19: chr6-32595223;