rs11962312

chr6-51508407-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 0.295 in 151,984 control chromosomes in the GnomAD database, including 7,499 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 0.30 (7499 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.74

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.44 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.295 AC: 44862 AN: 151866 Hom.: 7501 Cov.: 31

Gnomad AFR AF: 0.144

Gnomad AMI AF: 0.126

Gnomad AMR AF: 0.450

Gnomad ASJ AF: 0.348

Gnomad EAS AF: 0.193

Gnomad SAS AF: 0.318

Gnomad FIN AF: 0.343

Gnomad MID AF: 0.399

Gnomad NFE AF: 0.350

Gnomad OTH AF: 0.319

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

GnomAD4 genome AF: 0.295 AC: 44868 AN: 151984 Hom.: 7499 Cov.: 31 AF XY: 0.296 AC XY: 22015 AN XY: 74252

Gnomad4 AFR AF: 0.144

Gnomad4 AMR AF: 0.449

Gnomad4 ASJ AF: 0.348

Gnomad4 EAS AF: 0.193

Gnomad4 SAS AF: 0.320

Gnomad4 FIN AF: 0.343

Gnomad4 NFE AF: 0.350

Gnomad4 OTH AF: 0.317

Alfa AF: 0.352 Hom.: 12609

Bravo AF: 0.296

Asia WGS AF: 0.290 AC: 1007 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.55
Dann	Benign	0.20

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11962312; hg19: chr6-51373205;