ENST00000762706.1:n.404+24953A>G

Variant names:

• chr2-112795849-A-G
• rs6746923
• ENST00000762706.1:n.404+24953A>G

Variant summary

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

The ENST00000762706.1(ENSG00000299339):​n.404+24953A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.624 in 151,984 control chromosomes in the GnomAD database, including 29,763 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 0.62 (29763 hom., cov: 31)
• Consequence: ENSG00000299339 ENST00000762706.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.565
• Publications: 14 publications found

Genes affected

ENSG00000299339 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.768 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000762706.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000299339	ENST00000762706.1		n.404+24953A>G		intron	N/A
	ENSG00000299339	ENST00000762707.1		n.499+24953A>G		intron	N/A
	ENSG00000299339	ENST00000762708.1		n.265+24953A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.624 AC: 94723 AN: 151866 Hom.: 29725 Cov.: 31

Gnomad AFR AF: 0.601

Gnomad AMI AF: 0.635

Gnomad AMR AF: 0.691

Gnomad ASJ AF: 0.611

Gnomad EAS AF: 0.788

Gnomad SAS AF: 0.605

Gnomad FIN AF: 0.718

Gnomad MID AF: 0.601

Gnomad NFE AF: 0.597

Gnomad OTH AF: 0.620

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

GnomAD4 genome AF: 0.624 AC: 94816 AN: 151984 Hom.: 29763 Cov.: 31 AF XY: 0.633 AC XY: 47029 AN XY: 74304

African (AFR) AF: 0.601 AC: 24899 AN: 41416

American (AMR) AF: 0.691 AC: 10553 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.611 AC: 2118 AN: 3468

East Asian (EAS) AF: 0.788 AC: 4077 AN: 5174

South Asian (SAS) AF: 0.605 AC: 2912 AN: 4816

European-Finnish (FIN) AF: 0.718 AC: 7597 AN: 10578

Middle Eastern (MID) AF: 0.595 AC: 175 AN: 294

European-Non Finnish (NFE) AF: 0.597 AC: 40595 AN: 67958

Other (OTH) AF: 0.622 AC: 1313 AN: 2110

Alfa AF: 0.608 Hom.: 120418

Bravo AF: 0.624

Asia WGS AF: 0.691 AC: 2402 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	6.4
DANN	Benign	0.89
PhyloP100		-0.56

Splicing

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

Other links and lift over

dbSNP: rs6746923; hg19: chr2-113553426;