rs11962312

Variant names:

• chr6-51508407-T-C
• rs11962312

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 0.295 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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.144 AC: 5981 AN: 41484

American (AMR) AF: 0.449 AC: 6864 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.348 AC: 1206 AN: 3466

East Asian (EAS) AF: 0.193 AC: 997 AN: 5178

South Asian (SAS) AF: 0.320 AC: 1536 AN: 4806

European-Finnish (FIN) AF: 0.343 AC: 3609 AN: 10526

Middle Eastern (MID) AF: 0.395 AC: 116 AN: 294

European-Non Finnish (NFE) AF: 0.350 AC: 23775 AN: 67928

Other (OTH) AF: 0.317 AC: 669 AN: 2110

Alfa AF: 0.336 Hom.: 29970

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
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs11962312; hg19: chr6-51373205;