chr2-156916874-T-G

Variant names:

• chr2-156916874-T-G
• rs592582
• ENST00000762467.1:n.194+30312T>G

Variant summary

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

The ENST00000762467.1(ENSG00000287048):​n.194+30312T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.725 in 149,272 control chromosomes in the GnomAD database, including 42,416 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 0.73 (42416 hom., cov: 28)
• Consequence: ENSG00000287048 ENST00000762467.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.483
• Publications: 3 publications found

Genes affected

ENSG00000287048 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.71).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.871 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000762467.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000287048	ENST00000762467.1		n.194+30312T>G		intron	N/A
	ENSG00000287048	ENST00000762468.1		n.242+30312T>G		intron	N/A
	ENSG00000287048	ENST00000762469.1		n.362+30312T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.725 AC: 108231 AN: 149188 Hom.: 42409 Cov.: 28

Gnomad AFR AF: 0.405

Gnomad AMI AF: 0.874

Gnomad AMR AF: 0.752

Gnomad ASJ AF: 0.879

Gnomad EAS AF: 0.830

Gnomad SAS AF: 0.805

Gnomad FIN AF: 0.827

Gnomad MID AF: 0.793

Gnomad NFE AF: 0.877

Gnomad OTH AF: 0.732

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

GnomAD4 genome AF: 0.725 AC: 108259 AN: 149272 Hom.: 42416 Cov.: 28 AF XY: 0.725 AC XY: 52740 AN XY: 72720

African (AFR) AF: 0.405 AC: 16604 AN: 41040

American (AMR) AF: 0.753 AC: 11316 AN: 15030

Ashkenazi Jewish (ASJ) AF: 0.879 AC: 3032 AN: 3450

East Asian (EAS) AF: 0.830 AC: 4218 AN: 5084

South Asian (SAS) AF: 0.805 AC: 3834 AN: 4764

European-Finnish (FIN) AF: 0.827 AC: 7888 AN: 9542

Middle Eastern (MID) AF: 0.793 AC: 222 AN: 280

European-Non Finnish (NFE) AF: 0.877 AC: 58829 AN: 67100

Other (OTH) AF: 0.734 AC: 1524 AN: 2076

Alfa AF: 0.798 Hom.: 6300

Bravo AF: 0.708

Asia WGS AF: 0.774 AC: 2658 AN: 3438

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	7.9
DANN	Benign	0.90
PhyloP100		0.48

Splicing

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

Other links and lift over

dbSNP: rs592582; hg19: chr2-157773386;