11-86157598-T-C

Variant names:

• chr11-86157598-T-C
• rs3851179

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 0.691 in 152,074 control chromosomes in the GnomAD database, including 37,006 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 0.69 (37006 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.482
• Publications: 309 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.837 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: 0.691 AC: 104974 AN: 151956 Hom.: 36969 Cov.: 32

Gnomad AFR AF: 0.845

Gnomad AMI AF: 0.521

Gnomad AMR AF: 0.638

Gnomad ASJ AF: 0.606

Gnomad EAS AF: 0.603

Gnomad SAS AF: 0.610

Gnomad FIN AF: 0.648

Gnomad MID AF: 0.611

Gnomad NFE AF: 0.635

Gnomad OTH AF: 0.682

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

GnomAD4 genome AF: 0.691 AC: 105069 AN: 152074 Hom.: 37006 Cov.: 32 AF XY: 0.688 AC XY: 51121 AN XY: 74298

African (AFR) AF: 0.845 AC: 35072 AN: 41514

American (AMR) AF: 0.637 AC: 9724 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.606 AC: 2101 AN: 3468

East Asian (EAS) AF: 0.602 AC: 3119 AN: 5182

South Asian (SAS) AF: 0.612 AC: 2952 AN: 4822

European-Finnish (FIN) AF: 0.648 AC: 6826 AN: 10536

Middle Eastern (MID) AF: 0.616 AC: 181 AN: 294

European-Non Finnish (NFE) AF: 0.635 AC: 43180 AN: 67966

Other (OTH) AF: 0.682 AC: 1439 AN: 2110

Alfa AF: 0.650 Hom.: 143741

Bravo AF: 0.696

Asia WGS AF: 0.602 AC: 2093 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.8
DANN	Benign	0.73
PhyloP100		-0.48

Splicing

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

Other links and lift over

dbSNP: rs3851179; hg19: chr11-85868640;