2-70557529-C-G

Variant names:

• chr2-70557529-C-G
• rs13392762
• ENST00000726429.1:n.741+4137C>G

Variant summary

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

The ENST00000726429.1(ENSG00000294870):​n.741+4137C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.228 in 152,120 control chromosomes in the GnomAD database, including 4,339 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 0.23 (4339 hom., cov: 32)
• Consequence: ENSG00000294870 ENST00000726429.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.27
• Publications: 4 publications found

Genes affected

ENSG00000294870 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.25).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.297 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000726429.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000294870	ENST00000726429.1		n.741+4137C>G		intron	N/A
	ENSG00000294870	ENST00000726430.1		n.726+4129C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.228 AC: 34626 AN: 152002 Hom.: 4318 Cov.: 32

Gnomad AFR AF: 0.301

Gnomad AMI AF: 0.259

Gnomad AMR AF: 0.162

Gnomad ASJ AF: 0.214

Gnomad EAS AF: 0.288

Gnomad SAS AF: 0.254

Gnomad FIN AF: 0.170

Gnomad MID AF: 0.310

Gnomad NFE AF: 0.201

Gnomad OTH AF: 0.219

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

GnomAD4 genome AF: 0.228 AC: 34676 AN: 152120 Hom.: 4339 Cov.: 32 AF XY: 0.226 AC XY: 16811 AN XY: 74356

African (AFR) AF: 0.301 AC: 12500 AN: 41468

American (AMR) AF: 0.162 AC: 2478 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.214 AC: 743 AN: 3470

East Asian (EAS) AF: 0.288 AC: 1492 AN: 5174

South Asian (SAS) AF: 0.253 AC: 1220 AN: 4824

European-Finnish (FIN) AF: 0.170 AC: 1795 AN: 10568

Middle Eastern (MID) AF: 0.303 AC: 89 AN: 294

European-Non Finnish (NFE) AF: 0.201 AC: 13658 AN: 68008

Other (OTH) AF: 0.221 AC: 465 AN: 2104

Alfa AF: 0.102 Hom.: 160

Bravo AF: 0.229

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.25
CADD	Benign	16
DANN	Benign	0.83
PhyloP100		2.3

Splicing

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

Other links and lift over

dbSNP: rs13392762; hg19: chr2-70784661;