chr11-65637829-G-A

Variant names:

• chr11-65637829-G-A
• rs931127

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 0.491 in 152,094 control chromosomes in the GnomAD database, including 19,057 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 0.49 (19057 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.130
• Publications: 40 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.556 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: 0.491 AC: 74585 AN: 151976 Hom.: 19046 Cov.: 32

Gnomad AFR AF: 0.373

Gnomad AMI AF: 0.414

Gnomad AMR AF: 0.407

Gnomad ASJ AF: 0.566

Gnomad EAS AF: 0.456

Gnomad SAS AF: 0.573

Gnomad FIN AF: 0.638

Gnomad MID AF: 0.551

Gnomad NFE AF: 0.552

Gnomad OTH AF: 0.477

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

GnomAD4 genome AF: 0.491 AC: 74632 AN: 152094 Hom.: 19057 Cov.: 32 AF XY: 0.496 AC XY: 36856 AN XY: 74362

African (AFR) AF: 0.373 AC: 15475 AN: 41464

American (AMR) AF: 0.407 AC: 6214 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.566 AC: 1963 AN: 3468

East Asian (EAS) AF: 0.455 AC: 2354 AN: 5176

South Asian (SAS) AF: 0.574 AC: 2769 AN: 4828

European-Finnish (FIN) AF: 0.638 AC: 6750 AN: 10586

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

European-Non Finnish (NFE) AF: 0.552 AC: 37545 AN: 67968

Other (OTH) AF: 0.483 AC: 1022 AN: 2114

Alfa AF: 0.526 Hom.: 36829

Bravo AF: 0.462

Asia WGS AF: 0.517 AC: 1799 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	2.6
DANN	Benign	0.80
PhyloP100		-0.13
PromoterAI		-0.021	Neutral

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs931127; hg19: chr11-65405300;