rs6591255

Variant names:

• chr11-67582077-T-A
• rs6591255

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 0.375 in 152,092 control chromosomes in the GnomAD database, including 11,148 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 0.37 (11148 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.621
• Publications: 17 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.422 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: 0.375 AC: 56986 AN: 151974 Hom.: 11147 Cov.: 32

Gnomad AFR AF: 0.386

Gnomad AMI AF: 0.386

Gnomad AMR AF: 0.278

Gnomad ASJ AF: 0.261

Gnomad EAS AF: 0.158

Gnomad SAS AF: 0.296

Gnomad FIN AF: 0.320

Gnomad MID AF: 0.339

Gnomad NFE AF: 0.427

Gnomad OTH AF: 0.373

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

GnomAD4 genome AF: 0.375 AC: 57008 AN: 152092 Hom.: 11148 Cov.: 32 AF XY: 0.364 AC XY: 27052 AN XY: 74366

African (AFR) AF: 0.386 AC: 16023 AN: 41480

American (AMR) AF: 0.277 AC: 4234 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.261 AC: 904 AN: 3470

East Asian (EAS) AF: 0.158 AC: 816 AN: 5168

South Asian (SAS) AF: 0.295 AC: 1420 AN: 4814

European-Finnish (FIN) AF: 0.320 AC: 3386 AN: 10584

Middle Eastern (MID) AF: 0.330 AC: 97 AN: 294

European-Non Finnish (NFE) AF: 0.427 AC: 28998 AN: 67988

Other (OTH) AF: 0.369 AC: 779 AN: 2110

Alfa AF: 0.400 Hom.: 1636

Bravo AF: 0.372

Asia WGS AF: 0.254 AC: 886 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	2.0
DANN	Benign	0.35
PhyloP100		-0.62

Splicing

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

Other links and lift over

dbSNP: rs6591255; hg19: chr11-67349548;