rs3130695

Variant names:

• chr6-31243273-A-G
• rs3130695

Your query was ambiguous. Multiple possible variants found:

• chr6-31243273-A-G
• chr6-31243273-A-T

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 0.795 in 152,008 control chromosomes in the GnomAD database, including 48,024 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 0.79 (48024 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.22

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.802 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: 0.795 AC: 120730 AN: 151890 Hom.: 47987 Cov.: 31

Gnomad AFR AF: 0.810

Gnomad AMI AF: 0.837

Gnomad AMR AF: 0.785

Gnomad ASJ AF: 0.908

Gnomad EAS AF: 0.764

Gnomad SAS AF: 0.733

Gnomad FIN AF: 0.808

Gnomad MID AF: 0.807

Gnomad NFE AF: 0.786

Gnomad OTH AF: 0.801

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

GnomAD4 genome AF: 0.795 AC: 120816 AN: 152008 Hom.: 48024 Cov.: 31 AF XY: 0.794 AC XY: 59002 AN XY: 74298

Gnomad4 AFR AF: 0.810

Gnomad4 AMR AF: 0.785

Gnomad4 ASJ AF: 0.908

Gnomad4 EAS AF: 0.765

Gnomad4 SAS AF: 0.731

Gnomad4 FIN AF: 0.808

Gnomad4 NFE AF: 0.786

Gnomad4 OTH AF: 0.801

Alfa AF: 0.796 Hom.: 42430

Bravo AF: 0.793

Asia WGS AF: 0.757 AC: 2634 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.39
DANN	Benign	0.32

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3130695; hg19: chr6-31211050;