rs3998159

Variant names:

• chr6-32714242-A-C
• rs3998159

Your query was ambiguous. Multiple possible variants found:

• chr6-32714242-A-C
• chr6-32714242-A-G

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 0.093 in 152,086 control chromosomes in the GnomAD database, including 831 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 0.093 (831 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.506

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.177 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: 0.0930 AC: 14128 AN: 151968 Hom.: 830 Cov.: 32

Gnomad AFR AF: 0.0398

Gnomad AMI AF: 0.143

Gnomad AMR AF: 0.182

Gnomad ASJ AF: 0.169

Gnomad EAS AF: 0.0763

Gnomad SAS AF: 0.0687

Gnomad FIN AF: 0.111

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.101

Gnomad OTH AF: 0.0933

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

GnomAD4 genome AF: 0.0930 AC: 14148 AN: 152086 Hom.: 831 Cov.: 32 AF XY: 0.0950 AC XY: 7060 AN XY: 74352

Gnomad4 AFR AF: 0.0400

Gnomad4 AMR AF: 0.182

Gnomad4 ASJ AF: 0.169

Gnomad4 EAS AF: 0.0767

Gnomad4 SAS AF: 0.0686

Gnomad4 FIN AF: 0.111

Gnomad4 NFE AF: 0.101

Gnomad4 OTH AF: 0.0923

Alfa AF: 0.0973 Hom.: 1072

Bravo AF: 0.0999

Asia WGS AF: 0.0620 AC: 217 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	7.0
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3998159; hg19: chr6-32682019;