rs834830

Variant names:

• chr2-156346748-G-A
• rs834830
• ENST00000840148.1:n.104+4832G>A

Variant summary

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

The ENST00000840148.1(ENSG00000309294):​n.104+4832G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.717 in 152,114 control chromosomes in the GnomAD database, including 39,637 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 0.72 (39637 hom., cov: 32)
• Consequence: ENSG00000309294 ENST00000840148.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.986
• Publications: 6 publications found

Genes affected

ENSG00000309294 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.777 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
ENSG00000309294	ENST00000840148.1	n.104+4832G>A		intron_variant	Intron 1 of 2
ENSG00000309294	ENST00000840149.1	n.198-360G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.717 AC: 109014 AN: 151996 Hom.: 39626 Cov.: 32

Gnomad AFR AF: 0.659

Gnomad AMI AF: 0.771

Gnomad AMR AF: 0.616

Gnomad ASJ AF: 0.774

Gnomad EAS AF: 0.463

Gnomad SAS AF: 0.672

Gnomad FIN AF: 0.787

Gnomad MID AF: 0.680

Gnomad NFE AF: 0.783

Gnomad OTH AF: 0.725

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

GnomAD4 genome AF: 0.717 AC: 109065 AN: 152114 Hom.: 39637 Cov.: 32 AF XY: 0.714 AC XY: 53102 AN XY: 74386

African (AFR) AF: 0.659 AC: 27331 AN: 41470

American (AMR) AF: 0.615 AC: 9411 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.774 AC: 2688 AN: 3472

East Asian (EAS) AF: 0.463 AC: 2395 AN: 5174

South Asian (SAS) AF: 0.673 AC: 3244 AN: 4818

European-Finnish (FIN) AF: 0.787 AC: 8326 AN: 10578

Middle Eastern (MID) AF: 0.670 AC: 197 AN: 294

European-Non Finnish (NFE) AF: 0.783 AC: 53236 AN: 67984

Other (OTH) AF: 0.725 AC: 1535 AN: 2116

Alfa AF: 0.756 Hom.: 48659

Bravo AF: 0.695

Asia WGS AF: 0.613 AC: 2132 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.089
DANN	Benign	0.53
PhyloP100		-0.99

Splicing

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

Other links and lift over

dbSNP: rs834830; hg19: chr2-157203260;