chr3-43164470-G-A

Variant names:

• chr3-43164470-G-A
• rs2372342
• ENST00000730138.1:n.82+2040G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000730138.1(ENSG00000295441):​n.82+2040G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.871 in 152,118 control chromosomes in the GnomAD database, including 58,279 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 0.87 (58279 hom., cov: 31)
• Consequence: ENSG00000295441 ENST00000730138.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.24
• Publications: 3 publications found

Genes affected

ENSG00000295441 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.926 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
ENSG00000295441	ENST00000730138.1	n.82+2040G>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.871 AC: 132414 AN: 152002 Hom.: 58251 Cov.: 31

Gnomad AFR AF: 0.741

Gnomad AMI AF: 0.877

Gnomad AMR AF: 0.908

Gnomad ASJ AF: 0.867

Gnomad EAS AF: 0.837

Gnomad SAS AF: 0.850

Gnomad FIN AF: 0.964

Gnomad MID AF: 0.842

Gnomad NFE AF: 0.932

Gnomad OTH AF: 0.868

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

GnomAD4 genome AF: 0.871 AC: 132496 AN: 152118 Hom.: 58279 Cov.: 31 AF XY: 0.871 AC XY: 64743 AN XY: 74358

African (AFR) AF: 0.741 AC: 30689 AN: 41434

American (AMR) AF: 0.908 AC: 13889 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.867 AC: 3010 AN: 3472

East Asian (EAS) AF: 0.837 AC: 4311 AN: 5148

South Asian (SAS) AF: 0.851 AC: 4097 AN: 4816

European-Finnish (FIN) AF: 0.964 AC: 10231 AN: 10610

Middle Eastern (MID) AF: 0.854 AC: 251 AN: 294

European-Non Finnish (NFE) AF: 0.932 AC: 63395 AN: 68026

Other (OTH) AF: 0.865 AC: 1823 AN: 2108

Alfa AF: 0.911 Hom.: 117986

Bravo AF: 0.861

Asia WGS AF: 0.851 AC: 2960 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.51
DANN	Benign	0.69
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs2372342; hg19: chr3-43205962;