11-2934936-T-C

Position:

• chr11-2934936-T-C

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 0.264 in 152,064 control chromosomes in the GnomAD database, including 7,061 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 0.26 (7061 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.488

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.658 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.264 AC: 40077 AN: 151948 Hom.: 7049 Cov.: 31

Gnomad AFR AF: 0.0721

Gnomad AMI AF: 0.518

Gnomad AMR AF: 0.439

Gnomad ASJ AF: 0.361

Gnomad EAS AF: 0.676

Gnomad SAS AF: 0.400

Gnomad FIN AF: 0.224

Gnomad MID AF: 0.323

Gnomad NFE AF: 0.297

Gnomad OTH AF: 0.305

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

GnomAD4 genome AF: 0.264 AC: 40097 AN: 152064 Hom.: 7061 Cov.: 31 AF XY: 0.268 AC XY: 19921 AN XY: 74322

Gnomad4 AFR AF: 0.0720

Gnomad4 AMR AF: 0.440

Gnomad4 ASJ AF: 0.361

Gnomad4 EAS AF: 0.677

Gnomad4 SAS AF: 0.398

Gnomad4 FIN AF: 0.224

Gnomad4 NFE AF: 0.297

Gnomad4 OTH AF: 0.310

Alfa AF: 0.308 Hom.: 7370

Bravo AF: 0.273

Asia WGS AF: 0.499 AC: 1734 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.4
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2583442; hg19: chr11-2956166; COSMIC: COSV68664258;