rs3130695

Positions:

• 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;