11-68143316-G-T

Variant names:

• chr11-68143316-G-T
• rs2511470

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 0.656 in 152,020 control chromosomes in the GnomAD database, including 32,883 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 0.66 (32883 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.357
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.703 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: 0.656 AC: 99599 AN: 151902 Hom.: 32840 Cov.: 31

Gnomad AFR AF: 0.704

Gnomad AMI AF: 0.619

Gnomad AMR AF: 0.704

Gnomad ASJ AF: 0.684

Gnomad EAS AF: 0.684

Gnomad SAS AF: 0.725

Gnomad FIN AF: 0.625

Gnomad MID AF: 0.759

Gnomad NFE AF: 0.612

Gnomad OTH AF: 0.668

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

GnomAD4 genome AF: 0.656 AC: 99697 AN: 152020 Hom.: 32883 Cov.: 31 AF XY: 0.658 AC XY: 48917 AN XY: 74290

African (AFR) AF: 0.704 AC: 29171 AN: 41432

American (AMR) AF: 0.704 AC: 10750 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.684 AC: 2375 AN: 3470

East Asian (EAS) AF: 0.684 AC: 3531 AN: 5164

South Asian (SAS) AF: 0.723 AC: 3485 AN: 4820

European-Finnish (FIN) AF: 0.625 AC: 6613 AN: 10586

Middle Eastern (MID) AF: 0.759 AC: 223 AN: 294

European-Non Finnish (NFE) AF: 0.612 AC: 41573 AN: 67970

Other (OTH) AF: 0.670 AC: 1415 AN: 2112

Alfa AF: 0.640 Hom.: 51249

Bravo AF: 0.668

Asia WGS AF: 0.702 AC: 2445 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.88
DANN	Benign	0.37
PhyloP100		-0.36

Splicing

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

Other links and lift over

dbSNP: rs2511470; hg19: chr11-67910783; COSMIC: COSV51304831;