chr11-23221291-A-C

Variant names:

• chr11-23221291-A-C
• rs1038325

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 0.617 in 151,932 control chromosomes in the GnomAD database, including 29,137 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 (29137 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.866
• Publications: 1 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 (EAS) allele frequency at 95% confidence interval = 0.831 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: 0.617 AC: 93664 AN: 151814 Hom.: 29096 Cov.: 32

Gnomad AFR AF: 0.625

Gnomad AMI AF: 0.549

Gnomad AMR AF: 0.650

Gnomad ASJ AF: 0.483

Gnomad EAS AF: 0.851

Gnomad SAS AF: 0.578

Gnomad FIN AF: 0.582

Gnomad MID AF: 0.566

Gnomad NFE AF: 0.604

Gnomad OTH AF: 0.595

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

GnomAD4 genome AF: 0.617 AC: 93753 AN: 151932 Hom.: 29137 Cov.: 32 AF XY: 0.618 AC XY: 45886 AN XY: 74268

African (AFR) AF: 0.625 AC: 25894 AN: 41408

American (AMR) AF: 0.650 AC: 9914 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.483 AC: 1675 AN: 3470

East Asian (EAS) AF: 0.852 AC: 4417 AN: 5184

South Asian (SAS) AF: 0.579 AC: 2789 AN: 4818

European-Finnish (FIN) AF: 0.582 AC: 6130 AN: 10538

Middle Eastern (MID) AF: 0.561 AC: 165 AN: 294

European-Non Finnish (NFE) AF: 0.604 AC: 41013 AN: 67952

Other (OTH) AF: 0.596 AC: 1256 AN: 2106

Alfa AF: 0.609 Hom.: 47883

Bravo AF: 0.624

Asia WGS AF: 0.711 AC: 2473 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	0.76
DANN	Benign	0.65
PhyloP100		-0.87

Splicing

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

Other links and lift over

dbSNP: rs1038325; hg19: chr11-23242837;