6-32485414-T-C

Variant names:

• chr6-32485414-T-C
• rs6916742

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 0.513 in 150,370 control chromosomes in the GnomAD database, including 17,474 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 0.51 (17474 hom., cov: 37)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.188

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.568 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: 0.513 AC: 77096 AN: 150254 Hom.: 17460 Cov.: 37

Gnomad AFR AF: 0.417

Gnomad AMI AF: 0.679

Gnomad AMR AF: 0.578

Gnomad ASJ AF: 0.536

Gnomad EAS AF: 0.420

Gnomad SAS AF: 0.379

Gnomad FIN AF: 0.654

Gnomad MID AF: 0.418

Gnomad NFE AF: 0.549

Gnomad OTH AF: 0.515

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

GnomAD4 genome AF: 0.513 AC: 77143 AN: 150370 Hom.: 17474 Cov.: 37 AF XY: 0.515 AC XY: 37848 AN XY: 73528

Gnomad4 AFR AF: 0.417

Gnomad4 AMR AF: 0.578

Gnomad4 ASJ AF: 0.536

Gnomad4 EAS AF: 0.421

Gnomad4 SAS AF: 0.379

Gnomad4 FIN AF: 0.654

Gnomad4 NFE AF: 0.549

Gnomad4 OTH AF: 0.510

Alfa AF: 0.570 Hom.: 15721

Asia WGS AF: 0.367 AC: 1278 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.7
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6916742; hg19: chr6-32453191;