rs1834226

Variant names:

• chr2-162996953-T-G
• rs1834226
• ENST00000724875.1:n.266-25468A>C

Variant summary

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

The ENST00000724875.1(ENSG00000294636):​n.266-25468A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.173 in 152,144 control chromosomes in the GnomAD database, including 2,805 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 0.17 (2805 hom., cov: 32)
• Consequence: ENSG00000294636 ENST00000724875.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.366
• Publications: 0 publications found

Genes affected

ENSG00000294636 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.237 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
ENSG00000294636	ENST00000724875.1	n.266-25468A>C		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes AF: 0.173 AC: 26287 AN: 152028 Hom.: 2805 Cov.: 32

Gnomad AFR AF: 0.0488

Gnomad AMI AF: 0.201

Gnomad AMR AF: 0.196

Gnomad ASJ AF: 0.192

Gnomad EAS AF: 0.0891

Gnomad SAS AF: 0.103

Gnomad FIN AF: 0.251

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.241

Gnomad OTH AF: 0.189

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

GnomAD4 genome AF: 0.173 AC: 26274 AN: 152144 Hom.: 2805 Cov.: 32 AF XY: 0.174 AC XY: 12912 AN XY: 74366

African (AFR) AF: 0.0487 AC: 2024 AN: 41546

American (AMR) AF: 0.195 AC: 2980 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.192 AC: 665 AN: 3472

East Asian (EAS) AF: 0.0888 AC: 458 AN: 5160

South Asian (SAS) AF: 0.103 AC: 498 AN: 4822

European-Finnish (FIN) AF: 0.251 AC: 2656 AN: 10570

Middle Eastern (MID) AF: 0.214 AC: 63 AN: 294

European-Non Finnish (NFE) AF: 0.241 AC: 16352 AN: 67978

Other (OTH) AF: 0.188 AC: 395 AN: 2106

Alfa AF: 0.203 Hom.: 417

Bravo AF: 0.164

Asia WGS AF: 0.103 AC: 356 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	5.3
DANN	Benign	0.74
PhyloP100		0.37

Splicing

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

Other links and lift over

dbSNP: rs1834226; hg19: chr2-163853463;