ENST00000797860.1:n.42+2904A>G

Variant names:

• chr2-85737233-T-C
• rs4832006
• ENST00000797860.1:n.42+2904A>G

Variant summary

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

The ENST00000797860.1(ENSG00000303880):​n.42+2904A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.82 in 152,184 control chromosomes in the GnomAD database, including 51,182 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 0.82 (51182 hom., cov: 32)
• Consequence: ENSG00000303880 ENST00000797860.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.630
• Publications: 1 publications found

Genes affected

ENSG00000303880 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.84 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
ENSG00000303880	ENST00000797860.1	n.42+2904A>G		intron_variant	Intron 1 of 1
ENSG00000303899	ENST00000797924.1	n.77-916A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.820 AC: 124638 AN: 152066 Hom.: 51123 Cov.: 32

Gnomad AFR AF: 0.847

Gnomad AMI AF: 0.844

Gnomad AMR AF: 0.834

Gnomad ASJ AF: 0.795

Gnomad EAS AF: 0.732

Gnomad SAS AF: 0.680

Gnomad FIN AF: 0.805

Gnomad MID AF: 0.807

Gnomad NFE AF: 0.819

Gnomad OTH AF: 0.825

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

GnomAD4 genome AF: 0.820 AC: 124758 AN: 152184 Hom.: 51182 Cov.: 32 AF XY: 0.816 AC XY: 60737 AN XY: 74392

African (AFR) AF: 0.847 AC: 35183 AN: 41530

American (AMR) AF: 0.834 AC: 12766 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.795 AC: 2757 AN: 3470

East Asian (EAS) AF: 0.733 AC: 3781 AN: 5160

South Asian (SAS) AF: 0.682 AC: 3288 AN: 4824

European-Finnish (FIN) AF: 0.805 AC: 8528 AN: 10594

Middle Eastern (MID) AF: 0.803 AC: 236 AN: 294

European-Non Finnish (NFE) AF: 0.819 AC: 55703 AN: 67992

Other (OTH) AF: 0.828 AC: 1748 AN: 2110

Alfa AF: 0.821 Hom.: 197170

Bravo AF: 0.826

Asia WGS AF: 0.738 AC: 2567 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.4
DANN	Benign	0.65
PhyloP100		-0.63

Splicing

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

Other links and lift over

dbSNP: rs4832006; hg19: chr2-85964356;