11-68007631-A-G

Variant names:

• chr11-68007631-A-G
• rs3763942

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 0.143 in 152,088 control chromosomes in the GnomAD database, including 1,708 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 (1708 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.18 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: 0.143 AC: 21770 AN: 151970 Hom.: 1705 Cov.: 32

Gnomad AFR AF: 0.0916

Gnomad AMI AF: 0.295

Gnomad AMR AF: 0.142

Gnomad ASJ AF: 0.179

Gnomad EAS AF: 0.189

Gnomad SAS AF: 0.151

Gnomad FIN AF: 0.177

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.162

Gnomad OTH AF: 0.143

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

GnomAD4 genome AF: 0.143 AC: 21784 AN: 152088 Hom.: 1708 Cov.: 32 AF XY: 0.144 AC XY: 10673 AN XY: 74346

African (AFR) AF: 0.0915 AC: 3798 AN: 41500

American (AMR) AF: 0.142 AC: 2174 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.179 AC: 622 AN: 3470

East Asian (EAS) AF: 0.190 AC: 981 AN: 5166

South Asian (SAS) AF: 0.152 AC: 732 AN: 4820

European-Finnish (FIN) AF: 0.177 AC: 1875 AN: 10572

Middle Eastern (MID) AF: 0.0952 AC: 28 AN: 294

European-Non Finnish (NFE) AF: 0.162 AC: 11008 AN: 67966

Other (OTH) AF: 0.141 AC: 297 AN: 2108

Alfa AF: 0.144 Hom.: 688

Bravo AF: 0.137

Asia WGS AF: 0.158 AC: 550 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.8
DANN	Benign	0.64
PhyloP100		0.0

Splicing

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

Other links and lift over

dbSNP: rs3763942; hg19: chr11-67775101;