rs1033391

Variant names:

• chr6-113438861-C-T
• rs1033391

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 0.384 in 151,876 control chromosomes in the GnomAD database, including 11,632 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 0.38 (11632 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.359

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.434 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: 0.384 AC: 58227 AN: 151758 Hom.: 11621 Cov.: 31

Gnomad AFR AF: 0.288

Gnomad AMI AF: 0.417

Gnomad AMR AF: 0.417

Gnomad ASJ AF: 0.456

Gnomad EAS AF: 0.417

Gnomad SAS AF: 0.331

Gnomad FIN AF: 0.323

Gnomad MID AF: 0.566

Gnomad NFE AF: 0.438

Gnomad OTH AF: 0.455

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

GnomAD4 genome AF: 0.384 AC: 58274 AN: 151876 Hom.: 11632 Cov.: 31 AF XY: 0.378 AC XY: 28084 AN XY: 74226

Gnomad4 AFR AF: 0.288

Gnomad4 AMR AF: 0.417

Gnomad4 ASJ AF: 0.456

Gnomad4 EAS AF: 0.419

Gnomad4 SAS AF: 0.332

Gnomad4 FIN AF: 0.323

Gnomad4 NFE AF: 0.438

Gnomad4 OTH AF: 0.455

Alfa AF: 0.445 Hom.: 13667

Bravo AF: 0.389

Asia WGS AF: 0.344 AC: 1196 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.8
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1033391; hg19: chr6-113760063; COSMIC: COSV60268620;