rs3130955

Variant names:

• chr6-31086734-C-A
• rs3130955

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 0.348 in 152,048 control chromosomes in the GnomAD database, including 9,214 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 0.35 (9214 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.482
• Publications: 34 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.359 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.348 AC: 52881 AN: 151930 Hom.: 9196 Cov.: 32

Gnomad AFR AF: 0.351

Gnomad AMI AF: 0.475

Gnomad AMR AF: 0.307

Gnomad ASJ AF: 0.271

Gnomad EAS AF: 0.333

Gnomad SAS AF: 0.337

Gnomad FIN AF: 0.334

Gnomad MID AF: 0.306

Gnomad NFE AF: 0.363

Gnomad OTH AF: 0.325

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

GnomAD4 genome AF: 0.348 AC: 52940 AN: 152048 Hom.: 9214 Cov.: 32 AF XY: 0.348 AC XY: 25854 AN XY: 74332

African (AFR) AF: 0.351 AC: 14564 AN: 41448

American (AMR) AF: 0.308 AC: 4698 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.271 AC: 937 AN: 3462

East Asian (EAS) AF: 0.333 AC: 1721 AN: 5168

South Asian (SAS) AF: 0.336 AC: 1619 AN: 4814

European-Finnish (FIN) AF: 0.334 AC: 3531 AN: 10582

Middle Eastern (MID) AF: 0.305 AC: 89 AN: 292

European-Non Finnish (NFE) AF: 0.363 AC: 24652 AN: 67982

Other (OTH) AF: 0.330 AC: 697 AN: 2112

Alfa AF: 0.356 Hom.: 36628

Bravo AF: 0.348

Asia WGS AF: 0.333 AC: 1156 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.0
DANN	Benign	0.59
PhyloP100		-0.48

Splicing

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

Other links and lift over

dbSNP: rs3130955; hg19: chr6-31054511;