rs3130467

Variant names:

• chr6-31219298-C-T
• rs3130467

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.292 in 151,998 control chromosomes in the GnomAD database, including 6,588 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 0.29 (6588 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.105
• Publications: 31 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.383 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: 0.292 AC: 44327 AN: 151882 Hom.: 6581 Cov.: 32

Gnomad AFR AF: 0.325

Gnomad AMI AF: 0.366

Gnomad AMR AF: 0.253

Gnomad ASJ AF: 0.314

Gnomad EAS AF: 0.397

Gnomad SAS AF: 0.343

Gnomad FIN AF: 0.183

Gnomad MID AF: 0.320

Gnomad NFE AF: 0.283

Gnomad OTH AF: 0.297

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

GnomAD4 genome AF: 0.292 AC: 44362 AN: 151998 Hom.: 6588 Cov.: 32 AF XY: 0.287 AC XY: 21324 AN XY: 74276

African (AFR) AF: 0.325 AC: 13476 AN: 41452

American (AMR) AF: 0.253 AC: 3872 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.314 AC: 1087 AN: 3464

East Asian (EAS) AF: 0.397 AC: 2054 AN: 5172

South Asian (SAS) AF: 0.342 AC: 1645 AN: 4810

European-Finnish (FIN) AF: 0.183 AC: 1930 AN: 10538

Middle Eastern (MID) AF: 0.320 AC: 94 AN: 294

European-Non Finnish (NFE) AF: 0.283 AC: 19246 AN: 67964

Other (OTH) AF: 0.297 AC: 624 AN: 2104

Alfa AF: 0.290 Hom.: 26050

Bravo AF: 0.297

Asia WGS AF: 0.309 AC: 1078 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	8.5
DANN	Benign	0.86
PhyloP100		0.10

Splicing

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

Other links and lift over

dbSNP: rs3130467; hg19: chr6-31187075;