ENST00000846137.1:n.87-242C>T

Variant names:

• chr2-624678-G-A
• rs2903492
• ENST00000846137.1:n.87-242C>T

Variant summary

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

The ENST00000846137.1(ENSG00000309949):​n.87-242C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.85 in 152,208 control chromosomes in the GnomAD database, including 55,147 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 0.85 (55147 hom., cov: 32)
• Consequence: ENSG00000309949 ENST00000846137.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.313
• Publications: 30 publications found

Genes affected

ENSG00000309949 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.897 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
ENSG00000309949	ENST00000846137.1	n.87-242C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.850 AC: 129342 AN: 152090 Hom.: 55102 Cov.: 32

Gnomad AFR AF: 0.886

Gnomad AMI AF: 0.821

Gnomad AMR AF: 0.872

Gnomad ASJ AF: 0.744

Gnomad EAS AF: 0.919

Gnomad SAS AF: 0.805

Gnomad FIN AF: 0.848

Gnomad MID AF: 0.842

Gnomad NFE AF: 0.828

Gnomad OTH AF: 0.846

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

GnomAD4 genome AF: 0.850 AC: 129443 AN: 152208 Hom.: 55147 Cov.: 32 AF XY: 0.852 AC XY: 63369 AN XY: 74408

African (AFR) AF: 0.887 AC: 36841 AN: 41554

American (AMR) AF: 0.873 AC: 13339 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.744 AC: 2584 AN: 3472

East Asian (EAS) AF: 0.919 AC: 4749 AN: 5168

South Asian (SAS) AF: 0.803 AC: 3863 AN: 4810

European-Finnish (FIN) AF: 0.848 AC: 8978 AN: 10588

Middle Eastern (MID) AF: 0.830 AC: 244 AN: 294

European-Non Finnish (NFE) AF: 0.828 AC: 56304 AN: 68006

Other (OTH) AF: 0.847 AC: 1792 AN: 2116

Alfa AF: 0.841 Hom.: 86676

Bravo AF: 0.854

Asia WGS AF: 0.871 AC: 3032 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.7
DANN	Benign	0.34
PhyloP100		0.31

Splicing

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

Other links and lift over

dbSNP: rs2903492; hg19: chr2-624678;