rs3134774

Variant names:

• chr6-31233747-T-C
• rs3134774

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 152,162 control chromosomes in the GnomAD database, including 5,690 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 (5690 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.106
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• 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: 40695 AN: 152046 Hom.: 5690 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: 0.395

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: 40707 AN: 152162 Hom.: 5690 Cov.: 32 AF XY: 0.265 AC XY: 19718 AN XY: 74382

African (AFR) AF: 0.185 AC: 7699 AN: 41528

American (AMR) AF: 0.240 AC: 3664 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.323 AC: 1120 AN: 3470

East Asian (EAS) AF: 0.395 AC: 2045 AN: 5180

South Asian (SAS) AF: 0.283 AC: 1363 AN: 4820

European-Finnish (FIN) AF: 0.238 AC: 2523 AN: 10600

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

European-Non Finnish (NFE) AF: 0.313 AC: 21265 AN: 67972

Other (OTH) AF: 0.278 AC: 588 AN: 2112

Alfa AF: 0.289 Hom.: 808

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	-0.74
CADD	Benign	9.7
DANN	Benign	0.95
PhyloP100		0.11

Splicing

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

Other links and lift over

dbSNP: rs3134774; hg19: chr6-31201524;