rs1346760

Variant names:

• chr2-43218373-T-A
• rs1346760

Your query was ambiguous. Multiple possible variants found:

• chr2-43218373-T-A
• chr2-43218373-T-C

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.0679 in 152,260 control chromosomes in the GnomAD database, including 466 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 0.068 (466 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.16
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.23).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.131 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: 0.0680 AC: 10346 AN: 152142 Hom.: 466 Cov.: 33

Gnomad AFR AF: 0.0154

Gnomad AMI AF: 0.0559

Gnomad AMR AF: 0.0553

Gnomad ASJ AF: 0.0715

Gnomad EAS AF: 0.140

Gnomad SAS AF: 0.0806

Gnomad FIN AF: 0.121

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.0881

Gnomad OTH AF: 0.0679

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

GnomAD4 genome AF: 0.0679 AC: 10346 AN: 152260 Hom.: 466 Cov.: 33 AF XY: 0.0705 AC XY: 5245 AN XY: 74440

African (AFR) AF: 0.0154 AC: 640 AN: 41548

American (AMR) AF: 0.0553 AC: 847 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.0715 AC: 248 AN: 3470

East Asian (EAS) AF: 0.140 AC: 724 AN: 5180

South Asian (SAS) AF: 0.0803 AC: 387 AN: 4822

European-Finnish (FIN) AF: 0.121 AC: 1287 AN: 10598

Middle Eastern (MID) AF: 0.0952 AC: 28 AN: 294

European-Non Finnish (NFE) AF: 0.0880 AC: 5988 AN: 68018

Other (OTH) AF: 0.0691 AC: 146 AN: 2112

Alfa AF: 0.0894 Hom.: 90

Bravo AF: 0.0595

Asia WGS AF: 0.102 AC: 356 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.23
CADD	Benign	19
DANN	Benign	0.84
PhyloP100		3.2
Mutation Taster		=99/1	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs1346760; hg19: chr2-43445512;