rs641857

Variant names:

• chr11-102851320-G-T
• rs641857

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 0.101 in 152,100 control chromosomes in the GnomAD database, including 1,117 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 0.10 (1117 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.164
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.2 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: 0.101 AC: 15374 AN: 151982 Hom.: 1114 Cov.: 32

Gnomad AFR AF: 0.204

Gnomad AMI AF: 0.116

Gnomad AMR AF: 0.0697

Gnomad ASJ AF: 0.127

Gnomad EAS AF: 0.109

Gnomad SAS AF: 0.0956

Gnomad FIN AF: 0.0410

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.0528

Gnomad OTH AF: 0.100

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

GnomAD4 genome AF: 0.101 AC: 15379 AN: 152100 Hom.: 1117 Cov.: 32 AF XY: 0.0997 AC XY: 7414 AN XY: 74362

African (AFR) AF: 0.204 AC: 8461 AN: 41456

American (AMR) AF: 0.0695 AC: 1062 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.127 AC: 441 AN: 3470

East Asian (EAS) AF: 0.109 AC: 565 AN: 5176

South Asian (SAS) AF: 0.0945 AC: 455 AN: 4816

European-Finnish (FIN) AF: 0.0410 AC: 434 AN: 10576

Middle Eastern (MID) AF: 0.156 AC: 46 AN: 294

European-Non Finnish (NFE) AF: 0.0528 AC: 3589 AN: 68010

Other (OTH) AF: 0.104 AC: 220 AN: 2110

Alfa AF: 0.0815 Hom.: 91

Bravo AF: 0.108

Asia WGS AF: 0.109 AC: 380 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	4.5
DANN	Benign	0.76
PhyloP100		0.16

Splicing

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

Other links and lift over

dbSNP: rs641857; hg19: chr11-102722051;