rs3134646

Variant names:

• chr2-189015117-G-A
• rs3134646

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 0.415 in 152,058 control chromosomes in the GnomAD database, including 15,758 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 0.41 (15758 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.380
• Publications: 11 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.571 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: 0.415 AC: 63083 AN: 151938 Hom.: 15757 Cov.: 33

Gnomad AFR AF: 0.118

Gnomad AMI AF: 0.570

Gnomad AMR AF: 0.532

Gnomad ASJ AF: 0.421

Gnomad EAS AF: 0.589

Gnomad SAS AF: 0.447

Gnomad FIN AF: 0.592

Gnomad MID AF: 0.376

Gnomad NFE AF: 0.525

Gnomad OTH AF: 0.411

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

GnomAD4 genome AF: 0.415 AC: 63083 AN: 152058 Hom.: 15758 Cov.: 33 AF XY: 0.419 AC XY: 31160 AN XY: 74324

African (AFR) AF: 0.118 AC: 4878 AN: 41502

American (AMR) AF: 0.532 AC: 8121 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.421 AC: 1457 AN: 3464

East Asian (EAS) AF: 0.588 AC: 3044 AN: 5174

South Asian (SAS) AF: 0.447 AC: 2156 AN: 4818

European-Finnish (FIN) AF: 0.592 AC: 6250 AN: 10556

Middle Eastern (MID) AF: 0.384 AC: 112 AN: 292

European-Non Finnish (NFE) AF: 0.525 AC: 35685 AN: 67960

Other (OTH) AF: 0.408 AC: 862 AN: 2112

Alfa AF: 0.490 Hom.: 28194

Bravo AF: 0.400

Asia WGS AF: 0.486 AC: 1692 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.59
DANN	Benign	0.19
PhyloP100		-0.38

Splicing

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

Other links and lift over

dbSNP: rs3134646; hg19: chr2-189879843;