ENST00000762706.1:n.405-40276A>G

Variant names:

• chr2-112844982-A-G
• rs4849127
• ENST00000762706.1:n.405-40276A>G

Variant summary

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

The ENST00000762706.1(ENSG00000299339):​n.405-40276A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.879 in 152,084 control chromosomes in the GnomAD database, including 59,347 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 0.88 (59347 hom., cov: 30)
• Consequence: ENSG00000299339 ENST00000762706.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.631
• Publications: 9 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=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 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

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
	ENSG00000299339	ENST00000762706.1		n.405-40276A>G		intron	N/A
	ENSG00000299339	ENST00000762707.1		n.500-40276A>G		intron	N/A
	ENSG00000299339	ENST00000762708.1		n.266-40276A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.879 AC: 133580 AN: 151966 Hom.: 59305 Cov.: 30

Gnomad AFR AF: 0.741

Gnomad AMI AF: 0.995

Gnomad AMR AF: 0.921

Gnomad ASJ AF: 0.871

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.859

Gnomad FIN AF: 0.930

Gnomad MID AF: 0.823

Gnomad NFE AF: 0.937

Gnomad OTH AF: 0.879

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

GnomAD4 genome AF: 0.879 AC: 133676 AN: 152084 Hom.: 59347 Cov.: 30 AF XY: 0.880 AC XY: 65414 AN XY: 74338

African (AFR) AF: 0.741 AC: 30723 AN: 41454

American (AMR) AF: 0.921 AC: 14091 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.871 AC: 3023 AN: 3470

East Asian (EAS) AF: 1.00 AC: 5110 AN: 5112

South Asian (SAS) AF: 0.858 AC: 4133 AN: 4818

European-Finnish (FIN) AF: 0.930 AC: 9861 AN: 10604

Middle Eastern (MID) AF: 0.833 AC: 245 AN: 294

European-Non Finnish (NFE) AF: 0.937 AC: 63726 AN: 68010

Other (OTH) AF: 0.879 AC: 1859 AN: 2114

Alfa AF: 0.917 Hom.: 273683

Bravo AF: 0.874

Asia WGS AF: 0.910 AC: 3164 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.73
DANN	Benign	0.46
PhyloP100		-0.63

Splicing

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

Other links and lift over

dbSNP: rs4849127; hg19: chr2-113602559;