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. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.232

Gnomad4 AMR AF: 0.360

Gnomad4 ASJ AF: 0.466

Gnomad4 EAS AF: 0.356

Gnomad4 SAS AF: 0.340

Gnomad4 FIN AF: 0.521

Gnomad4 NFE AF: 0.493

Gnomad4 OTH AF: 0.407

Alfa AF: 0.459 Hom.: 13205

Bravo AF: 0.377

Asia WGS AF: 0.341 AC: 1183 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1346004; hg19: chr2-166601046;