rs1346004

Variant names:

• chr2-165744536-G-A
• rs1346004

Your query was ambiguous. Multiple possible variants found:

• chr2-165744536-G-A
• chr2-165744536-G-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 0.399 in 151,980 control chromosomes in the GnomAD database, including 13,220 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 0.40 (13220 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.589
• Publications: 33 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.488 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.399 AC: 60661 AN: 151862 Hom.: 13209 Cov.: 31

Gnomad AFR AF: 0.232

Gnomad AMI AF: 0.610

Gnomad AMR AF: 0.361

Gnomad ASJ AF: 0.466

Gnomad EAS AF: 0.356

Gnomad SAS AF: 0.339

Gnomad FIN AF: 0.521

Gnomad MID AF: 0.347

Gnomad NFE AF: 0.493

Gnomad OTH AF: 0.403

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

GnomAD4 genome AF: 0.399 AC: 60693 AN: 151980 Hom.: 13220 Cov.: 31 AF XY: 0.402 AC XY: 29870 AN XY: 74292

African (AFR) AF: 0.232 AC: 9621 AN: 41466

American (AMR) AF: 0.360 AC: 5497 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.466 AC: 1614 AN: 3464

East Asian (EAS) AF: 0.356 AC: 1843 AN: 5170

South Asian (SAS) AF: 0.340 AC: 1642 AN: 4830

European-Finnish (FIN) AF: 0.521 AC: 5499 AN: 10560

Middle Eastern (MID) AF: 0.349 AC: 102 AN: 292

European-Non Finnish (NFE) AF: 0.493 AC: 33465 AN: 67926

Other (OTH) AF: 0.407 AC: 859 AN: 2112

Alfa AF: 0.454 Hom.: 43469

Bravo AF: 0.377

Asia WGS AF: 0.341 AC: 1183 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.43
DANN	Benign	0.55
PhyloP100		-0.59

Splicing

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

Other links and lift over

dbSNP: rs1346004; hg19: chr2-166601046;