3-127037647-G-A

Variant names:

• chr3-127037647-G-A
• rs17751931

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 0.115 in 152,254 control chromosomes in the GnomAD database, including 1,060 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 0.11 (1060 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.286
• Publications: 0 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 = 0.133 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: 0.115 AC: 17457 AN: 152136 Hom.: 1060 Cov.: 33

Gnomad AFR AF: 0.0999

Gnomad AMI AF: 0.230

Gnomad AMR AF: 0.105

Gnomad ASJ AF: 0.182

Gnomad EAS AF: 0.00501

Gnomad SAS AF: 0.0518

Gnomad FIN AF: 0.0975

Gnomad MID AF: 0.222

Gnomad NFE AF: 0.136

Gnomad OTH AF: 0.134

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

GnomAD4 genome AF: 0.115 AC: 17469 AN: 152254 Hom.: 1060 Cov.: 33 AF XY: 0.112 AC XY: 8309 AN XY: 74424

African (AFR) AF: 0.0999 AC: 4153 AN: 41556

American (AMR) AF: 0.105 AC: 1601 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.182 AC: 630 AN: 3470

East Asian (EAS) AF: 0.00483 AC: 25 AN: 5178

South Asian (SAS) AF: 0.0525 AC: 253 AN: 4822

European-Finnish (FIN) AF: 0.0975 AC: 1033 AN: 10598

Middle Eastern (MID) AF: 0.224 AC: 66 AN: 294

European-Non Finnish (NFE) AF: 0.136 AC: 9219 AN: 68018

Other (OTH) AF: 0.132 AC: 280 AN: 2114

Alfa AF: 0.131 Hom.: 708

Bravo AF: 0.117

Asia WGS AF: 0.0340 AC: 122 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	2.7
DANN	Benign	0.40
PhyloP100		0.29

Splicing

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

Other links and lift over

dbSNP: rs17751931; hg19: chr3-126756490;