11-106042257-T-C

Variant names:

• chr11-106042257-T-C
• rs6591147

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 0.597 in 151,964 control chromosomes in the GnomAD database, including 27,109 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 0.60 (27109 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.221
• Publications: 10 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.609 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: 0.597 AC: 90612 AN: 151846 Hom.: 27099 Cov.: 32

Gnomad AFR AF: 0.584

Gnomad AMI AF: 0.532

Gnomad AMR AF: 0.620

Gnomad ASJ AF: 0.553

Gnomad EAS AF: 0.561

Gnomad SAS AF: 0.617

Gnomad FIN AF: 0.551

Gnomad MID AF: 0.563

Gnomad NFE AF: 0.611

Gnomad OTH AF: 0.594

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

GnomAD4 genome AF: 0.597 AC: 90654 AN: 151964 Hom.: 27109 Cov.: 32 AF XY: 0.593 AC XY: 44070 AN XY: 74266

African (AFR) AF: 0.584 AC: 24206 AN: 41460

American (AMR) AF: 0.620 AC: 9461 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.553 AC: 1914 AN: 3464

East Asian (EAS) AF: 0.559 AC: 2875 AN: 5142

South Asian (SAS) AF: 0.618 AC: 2977 AN: 4820

European-Finnish (FIN) AF: 0.551 AC: 5825 AN: 10568

Middle Eastern (MID) AF: 0.551 AC: 162 AN: 294

European-Non Finnish (NFE) AF: 0.611 AC: 41505 AN: 67936

Other (OTH) AF: 0.592 AC: 1246 AN: 2106

Alfa AF: 0.606 Hom.: 32286

Bravo AF: 0.603

Asia WGS AF: 0.568 AC: 1977 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.8
DANN	Benign	0.54
PhyloP100		-0.22

Splicing

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

Other links and lift over

dbSNP: rs6591147; hg19: chr11-105912984;