11-32346911-A-T

Variant names:

• chr11-32346911-A-T
• rs2207549

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 0.465 in 152,020 control chromosomes in the GnomAD database, including 17,885 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 0.47 (17885 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.617
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.661 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.465 AC: 70683 AN: 151902 Hom.: 17852 Cov.: 32

Gnomad AFR AF: 0.667

Gnomad AMI AF: 0.227

Gnomad AMR AF: 0.324

Gnomad ASJ AF: 0.407

Gnomad EAS AF: 0.157

Gnomad SAS AF: 0.321

Gnomad FIN AF: 0.348

Gnomad MID AF: 0.443

Gnomad NFE AF: 0.433

Gnomad OTH AF: 0.457

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

GnomAD4 genome AF: 0.465 AC: 70753 AN: 152020 Hom.: 17885 Cov.: 32 AF XY: 0.455 AC XY: 33778 AN XY: 74302

African (AFR) AF: 0.667 AC: 27665 AN: 41470

American (AMR) AF: 0.324 AC: 4946 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.407 AC: 1411 AN: 3470

East Asian (EAS) AF: 0.157 AC: 810 AN: 5162

South Asian (SAS) AF: 0.321 AC: 1547 AN: 4820

European-Finnish (FIN) AF: 0.348 AC: 3673 AN: 10562

Middle Eastern (MID) AF: 0.449 AC: 132 AN: 294

European-Non Finnish (NFE) AF: 0.433 AC: 29404 AN: 67946

Other (OTH) AF: 0.454 AC: 958 AN: 2108

Alfa AF: 0.446 Hom.: 1902

Bravo AF: 0.470

Asia WGS AF: 0.307 AC: 1065 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	2.2
DANN	Benign	0.71
PhyloP100		-0.62

Splicing

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

Other links and lift over

dbSNP: rs2207549; hg19: chr11-32368457; COSMIC: COSV73227965;