rs6591256

Variant names:

• chr11-67582428-A-G
• rs6591256

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 152,082 control chromosomes in the GnomAD database, including 11,124 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 (11124 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.319
• Publications: 48 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.422 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.375 AC: 56935 AN: 151964 Hom.: 11123 Cov.: 32

Gnomad AFR AF: 0.386

Gnomad AMI AF: 0.385

Gnomad AMR AF: 0.278

Gnomad ASJ AF: 0.260

Gnomad EAS AF: 0.158

Gnomad SAS AF: 0.297

Gnomad FIN AF: 0.320

Gnomad MID AF: 0.339

Gnomad NFE AF: 0.426

Gnomad OTH AF: 0.372

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

GnomAD4 genome AF: 0.375 AC: 56957 AN: 152082 Hom.: 11124 Cov.: 32 AF XY: 0.363 AC XY: 27015 AN XY: 74340

African (AFR) AF: 0.386 AC: 16010 AN: 41466

American (AMR) AF: 0.277 AC: 4234 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.260 AC: 904 AN: 3472

East Asian (EAS) AF: 0.158 AC: 820 AN: 5186

South Asian (SAS) AF: 0.296 AC: 1426 AN: 4820

European-Finnish (FIN) AF: 0.320 AC: 3382 AN: 10584

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

European-Non Finnish (NFE) AF: 0.426 AC: 28958 AN: 67968

Other (OTH) AF: 0.368 AC: 776 AN: 2106

Alfa AF: 0.398 Hom.: 19407

Bravo AF: 0.372

Asia WGS AF: 0.253 AC: 884 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	4.1
DANN	Benign	0.32
PhyloP100		0.32

Splicing

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

Other links and lift over

dbSNP: rs6591256; hg19: chr11-67349899;