chr11-102877720-A-G

Variant names:

• chr11-102877720-A-G
• rs501371

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 0.136 in 152,166 control chromosomes in the GnomAD database, including 2,446 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 0.14 (2446 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.100
• Publications: 8 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 = 0.318 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.135 AC: 20602 AN: 152046 Hom.: 2438 Cov.: 32

Gnomad AFR AF: 0.323

Gnomad AMI AF: 0.114

Gnomad AMR AF: 0.0847

Gnomad ASJ AF: 0.128

Gnomad EAS AF: 0.109

Gnomad SAS AF: 0.0938

Gnomad FIN AF: 0.0407

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.0536

Gnomad OTH AF: 0.126

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

GnomAD4 genome AF: 0.136 AC: 20624 AN: 152166 Hom.: 2446 Cov.: 32 AF XY: 0.133 AC XY: 9876 AN XY: 74388

African (AFR) AF: 0.322 AC: 13374 AN: 41470

American (AMR) AF: 0.0845 AC: 1291 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.128 AC: 444 AN: 3470

East Asian (EAS) AF: 0.109 AC: 566 AN: 5174

South Asian (SAS) AF: 0.0927 AC: 447 AN: 4824

European-Finnish (FIN) AF: 0.0407 AC: 432 AN: 10620

Middle Eastern (MID) AF: 0.163 AC: 48 AN: 294

European-Non Finnish (NFE) AF: 0.0536 AC: 3643 AN: 68004

Other (OTH) AF: 0.130 AC: 275 AN: 2114

Alfa AF: 0.0776 Hom.: 628

Bravo AF: 0.147

Asia WGS AF: 0.115 AC: 401 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.4
DANN	Benign	0.65
PhyloP100		-0.10

Splicing

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

Other links and lift over

dbSNP: rs501371; hg19: chr11-102748450;