chr11-13248667-A-G

Variant names:

• chr11-13248667-A-G
• rs11605518

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 0.712 in 152,112 control chromosomes in the GnomAD database, including 38,683 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 0.71 (38683 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.52
• Publications: 11 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.731 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: 0.712 AC: 108164 AN: 151994 Hom.: 38632 Cov.: 32

Gnomad AFR AF: 0.737

Gnomad AMI AF: 0.606

Gnomad AMR AF: 0.669

Gnomad ASJ AF: 0.714

Gnomad EAS AF: 0.497

Gnomad SAS AF: 0.653

Gnomad FIN AF: 0.740

Gnomad MID AF: 0.665

Gnomad NFE AF: 0.723

Gnomad OTH AF: 0.713

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

GnomAD4 genome AF: 0.712 AC: 108276 AN: 152112 Hom.: 38683 Cov.: 32 AF XY: 0.712 AC XY: 52902 AN XY: 74346

African (AFR) AF: 0.738 AC: 30617 AN: 41510

American (AMR) AF: 0.669 AC: 10209 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.714 AC: 2480 AN: 3472

East Asian (EAS) AF: 0.497 AC: 2571 AN: 5178

South Asian (SAS) AF: 0.656 AC: 3161 AN: 4818

European-Finnish (FIN) AF: 0.740 AC: 7825 AN: 10576

Middle Eastern (MID) AF: 0.656 AC: 193 AN: 294

European-Non Finnish (NFE) AF: 0.723 AC: 49159 AN: 67986

Other (OTH) AF: 0.717 AC: 1511 AN: 2108

Alfa AF: 0.719 Hom.: 17409

Bravo AF: 0.711

Asia WGS AF: 0.593 AC: 2055 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.53
DANN	Benign	0.42
PhyloP100		-3.5

Splicing

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

Other links and lift over

dbSNP: rs11605518; hg19: chr11-13270214;