2-118285633-G-A

Variant names:

• chr2-118285633-G-A
• rs9308765
• ENST00000807542.1:n.839+28716G>A

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000807542.1(ENSG00000304983):​n.839+28716G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.165 in 152,028 control chromosomes in the GnomAD database, including 2,541 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 0.16 (2541 hom., cov: 32)
• Consequence: ENSG00000304983 ENST00000807542.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.136
• Publications: 11 publications found

Genes affected

ENSG00000304983 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.29).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.286 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000807542.1. 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
	ENSG00000304983	ENST00000807542.1		n.839+28716G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.165 AC: 25041 AN: 151910 Hom.: 2534 Cov.: 32

Gnomad AFR AF: 0.290

Gnomad AMI AF: 0.0285

Gnomad AMR AF: 0.117

Gnomad ASJ AF: 0.108

Gnomad EAS AF: 0.165

Gnomad SAS AF: 0.174

Gnomad FIN AF: 0.0858

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.116

Gnomad OTH AF: 0.142

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

GnomAD4 genome AF: 0.165 AC: 25078 AN: 152028 Hom.: 2541 Cov.: 32 AF XY: 0.164 AC XY: 12156 AN XY: 74320

African (AFR) AF: 0.290 AC: 12033 AN: 41450

American (AMR) AF: 0.117 AC: 1792 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.108 AC: 373 AN: 3468

East Asian (EAS) AF: 0.164 AC: 847 AN: 5170

South Asian (SAS) AF: 0.174 AC: 837 AN: 4812

European-Finnish (FIN) AF: 0.0858 AC: 907 AN: 10576

Middle Eastern (MID) AF: 0.224 AC: 66 AN: 294

European-Non Finnish (NFE) AF: 0.116 AC: 7901 AN: 67978

Other (OTH) AF: 0.141 AC: 296 AN: 2102

Alfa AF: 0.127 Hom.: 2786

Bravo AF: 0.170

Asia WGS AF: 0.134 AC: 466 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.29
CADD	Benign	13
DANN	Benign	0.81
PhyloP100		-0.14

Splicing

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

Other links and lift over

dbSNP: rs9308765; hg19: chr2-119043209;