11-32346911-A-T

Variant names:

• chr11-32346911-A-T
• rs2207549

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.465 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

Gnomad4 AFR AF: 0.667

Gnomad4 AMR AF: 0.324

Gnomad4 ASJ AF: 0.407

Gnomad4 EAS AF: 0.157

Gnomad4 SAS AF: 0.321

Gnomad4 FIN AF: 0.348

Gnomad4 NFE AF: 0.433

Gnomad4 OTH AF: 0.454

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

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