rs1346004

Positions:

• 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;