rs9271588

chr6-32623176-T-C

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 0.436 in 151,984 control chromosomes in the GnomAD database, including 14,832 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 0.44 (14832 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.11

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.463 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: 0.436 AC: 66139 AN: 151866 Hom.: 14817 Cov.: 32

Gnomad AFR AF: 0.360

Gnomad AMI AF: 0.670

Gnomad AMR AF: 0.472

Gnomad ASJ AF: 0.502

Gnomad EAS AF: 0.448

Gnomad SAS AF: 0.417

Gnomad FIN AF: 0.463

Gnomad MID AF: 0.399

Gnomad NFE AF: 0.462

Gnomad OTH AF: 0.454

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

GnomAD4 genome AF: 0.436 AC: 66196 AN: 151984 Hom.: 14832 Cov.: 32 AF XY: 0.434 AC XY: 32274 AN XY: 74294

Gnomad4 AFR AF: 0.360

Gnomad4 AMR AF: 0.472

Gnomad4 ASJ AF: 0.502

Gnomad4 EAS AF: 0.449

Gnomad4 SAS AF: 0.419

Gnomad4 FIN AF: 0.463

Gnomad4 NFE AF: 0.462

Gnomad4 OTH AF: 0.452

Alfa AF: 0.462 Hom.: 20328

Bravo AF: 0.439

Asia WGS AF: 0.395 AC: 1379 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	2.3
Dann	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9271588; hg19: chr6-32590953;