rs3134775

Variant names:

• chr6-31233580-A-C
• rs3134775

Your query was ambiguous. Multiple possible variants found:

• chr6-31233580-A-C
• chr6-31233580-A-T

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 0.268 in 152,142 control chromosomes in the GnomAD database, including 5,684 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 0.27 (5684 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.118
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.381 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: 0.268 AC: 40689 AN: 152024 Hom.: 5684 Cov.: 32

Gnomad AFR AF: 0.185

Gnomad AMI AF: 0.393

Gnomad AMR AF: 0.240

Gnomad ASJ AF: 0.323

Gnomad EAS AF: 0.396

Gnomad SAS AF: 0.284

Gnomad FIN AF: 0.238

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.313

Gnomad OTH AF: 0.278

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

GnomAD4 genome AF: 0.268 AC: 40702 AN: 152142 Hom.: 5684 Cov.: 32 AF XY: 0.265 AC XY: 19702 AN XY: 74356

African (AFR) AF: 0.185 AC: 7701 AN: 41518

American (AMR) AF: 0.240 AC: 3664 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.323 AC: 1120 AN: 3468

East Asian (EAS) AF: 0.396 AC: 2046 AN: 5172

South Asian (SAS) AF: 0.283 AC: 1366 AN: 4824

European-Finnish (FIN) AF: 0.238 AC: 2512 AN: 10576

Middle Eastern (MID) AF: 0.279 AC: 82 AN: 294

European-Non Finnish (NFE) AF: 0.313 AC: 21265 AN: 67978

Other (OTH) AF: 0.279 AC: 588 AN: 2110

Alfa AF: 0.165 Hom.: 349

Bravo AF: 0.264

Asia WGS AF: 0.281 AC: 979 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	5.9
DANN	Benign	0.63
PhyloP100		0.12

Splicing

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

Other links and lift over

dbSNP: rs3134775; hg19: chr6-31201357;