rs743862

Variant names:

• chr6-32414162-T-C
• rs743862

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 0.303 in 152,068 control chromosomes in the GnomAD database, including 7,470 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 (7470 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.335

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.328 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: 0.303 AC: 46105 AN: 151950 Hom.: 7463 Cov.: 31

Gnomad AFR AF: 0.306

Gnomad AMI AF: 0.501

Gnomad AMR AF: 0.239

Gnomad ASJ AF: 0.153

Gnomad EAS AF: 0.0827

Gnomad SAS AF: 0.154

Gnomad FIN AF: 0.422

Gnomad MID AF: 0.156

Gnomad NFE AF: 0.331

Gnomad OTH AF: 0.285

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

GnomAD4 genome AF: 0.303 AC: 46134 AN: 152068 Hom.: 7470 Cov.: 31 AF XY: 0.299 AC XY: 22230 AN XY: 74314

Gnomad4 AFR AF: 0.306

Gnomad4 AMR AF: 0.239

Gnomad4 ASJ AF: 0.153

Gnomad4 EAS AF: 0.0825

Gnomad4 SAS AF: 0.154

Gnomad4 FIN AF: 0.422

Gnomad4 NFE AF: 0.331

Gnomad4 OTH AF: 0.282

Alfa AF: 0.324 Hom.: 4751

Bravo AF: 0.290

Asia WGS AF: 0.140 AC: 488 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.8
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs743862; hg19: chr6-32381939;