11-68143161-A-G

Variant names:

• chr11-68143161-A-G
• rs2511472

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 0.518 in 151,956 control chromosomes in the GnomAD database, including 21,606 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 0.52 (21606 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.240
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.659 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: 0.518 AC: 78627 AN: 151838 Hom.: 21596 Cov.: 32

Gnomad AFR AF: 0.316

Gnomad AMI AF: 0.538

Gnomad AMR AF: 0.643

Gnomad ASJ AF: 0.608

Gnomad EAS AF: 0.666

Gnomad SAS AF: 0.679

Gnomad FIN AF: 0.597

Gnomad MID AF: 0.699

Gnomad NFE AF: 0.570

Gnomad OTH AF: 0.560

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

GnomAD4 genome AF: 0.518 AC: 78651 AN: 151956 Hom.: 21606 Cov.: 32 AF XY: 0.524 AC XY: 38916 AN XY: 74266

African (AFR) AF: 0.315 AC: 13067 AN: 41438

American (AMR) AF: 0.644 AC: 9830 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.608 AC: 2110 AN: 3470

East Asian (EAS) AF: 0.666 AC: 3435 AN: 5154

South Asian (SAS) AF: 0.678 AC: 3267 AN: 4816

European-Finnish (FIN) AF: 0.597 AC: 6292 AN: 10546

Middle Eastern (MID) AF: 0.694 AC: 204 AN: 294

European-Non Finnish (NFE) AF: 0.571 AC: 38767 AN: 67944

Other (OTH) AF: 0.563 AC: 1189 AN: 2112

Alfa AF: 0.553 Hom.: 4824

Bravo AF: 0.518

Asia WGS AF: 0.636 AC: 2211 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	12
DANN	Benign	0.66
PhyloP100		0.24

Splicing

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

Other links and lift over

dbSNP: rs2511472; hg19: chr11-67910628;