rs642093

Variant names:

• chr6-32614298-G-A
• rs642093

Your query was ambiguous. Multiple possible variants found:

• chr6-32614298-G-A
• chr6-32614298-G-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 0.263 in 151,990 control chromosomes in the GnomAD database, including 5,560 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 0.26 (5560 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.38

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.303 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: 0.263 AC: 39978 AN: 151872 Hom.: 5558 Cov.: 31

Gnomad AFR AF: 0.308

Gnomad AMI AF: 0.167

Gnomad AMR AF: 0.240

Gnomad ASJ AF: 0.281

Gnomad EAS AF: 0.299

Gnomad SAS AF: 0.214

Gnomad FIN AF: 0.208

Gnomad MID AF: 0.399

Gnomad NFE AF: 0.250

Gnomad OTH AF: 0.276

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

GnomAD4 genome AF: 0.263 AC: 40003 AN: 151990 Hom.: 5560 Cov.: 31 AF XY: 0.260 AC XY: 19333 AN XY: 74284

Gnomad4 AFR AF: 0.308

Gnomad4 AMR AF: 0.239

Gnomad4 ASJ AF: 0.281

Gnomad4 EAS AF: 0.299

Gnomad4 SAS AF: 0.215

Gnomad4 FIN AF: 0.208

Gnomad4 NFE AF: 0.250

Gnomad4 OTH AF: 0.275

Alfa AF: 0.255 Hom.: 6315

Bravo AF: 0.267

Asia WGS AF: 0.211 AC: 734 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	9.4
DANN	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs642093; hg19: chr6-32582075;