chr11-13272293-G-A

Variant names:

• chr11-13272293-G-A
• rs900147

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 0.62 in 152,034 control chromosomes in the GnomAD database, including 30,106 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 0.62 (30106 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.05
• Publications: 18 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.697 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: 0.620 AC: 94182 AN: 151916 Hom.: 30073 Cov.: 33

Gnomad AFR AF: 0.463

Gnomad AMI AF: 0.609

Gnomad AMR AF: 0.618

Gnomad ASJ AF: 0.661

Gnomad EAS AF: 0.537

Gnomad SAS AF: 0.634

Gnomad FIN AF: 0.723

Gnomad MID AF: 0.608

Gnomad NFE AF: 0.703

Gnomad OTH AF: 0.637

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

GnomAD4 genome AF: 0.620 AC: 94268 AN: 152034 Hom.: 30106 Cov.: 33 AF XY: 0.622 AC XY: 46255 AN XY: 74306

African (AFR) AF: 0.463 AC: 19200 AN: 41426

American (AMR) AF: 0.618 AC: 9449 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.661 AC: 2293 AN: 3470

East Asian (EAS) AF: 0.536 AC: 2779 AN: 5182

South Asian (SAS) AF: 0.637 AC: 3073 AN: 4824

European-Finnish (FIN) AF: 0.723 AC: 7633 AN: 10552

Middle Eastern (MID) AF: 0.592 AC: 174 AN: 294

European-Non Finnish (NFE) AF: 0.703 AC: 47762 AN: 67984

Other (OTH) AF: 0.640 AC: 1351 AN: 2110

Alfa AF: 0.573 Hom.: 1860

Bravo AF: 0.607

Asia WGS AF: 0.605 AC: 2104 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.79
DANN	Benign	0.60
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs900147; hg19: chr11-13293840;