rs6591255

chr11-67582077-T-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 0.375 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.386

Gnomad4 AMR AF: 0.277

Gnomad4 ASJ AF: 0.261

Gnomad4 EAS AF: 0.158

Gnomad4 SAS AF: 0.295

Gnomad4 FIN AF: 0.320

Gnomad4 NFE AF: 0.427

Gnomad4 OTH AF: 0.369

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6591255; hg19: chr11-67349548;