chr2-117576666-C-T

Variant names:

• chr2-117576666-C-T
• rs1516003
• ENST00000752778.1:n.462+46569G>A

Variant summary

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

The ENST00000752778.1(ENSG00000298065):​n.462+46569G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.501 in 152,004 control chromosomes in the GnomAD database, including 22,529 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 0.50 (22529 hom., cov: 32)
• Consequence: ENSG00000298065 ENST00000752778.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.991
• Publications: 3 publications found

Genes affected

ENSG00000298065 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.52).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.647 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000752778.1. 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
	ENSG00000298065	ENST00000752778.1		n.462+46569G>A		intron	N/A
	ENSG00000298065	ENST00000752779.1		n.535+46569G>A		intron	N/A
	ENSG00000298065	ENST00000752780.1		n.377+46569G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.501 AC: 76156 AN: 151886 Hom.: 22526 Cov.: 32

Gnomad AFR AF: 0.170

Gnomad AMI AF: 0.507

Gnomad AMR AF: 0.520

Gnomad ASJ AF: 0.674

Gnomad EAS AF: 0.557

Gnomad SAS AF: 0.516

Gnomad FIN AF: 0.697

Gnomad MID AF: 0.633

Gnomad NFE AF: 0.652

Gnomad OTH AF: 0.549

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

GnomAD4 genome AF: 0.501 AC: 76155 AN: 152004 Hom.: 22529 Cov.: 32 AF XY: 0.504 AC XY: 37473 AN XY: 74296

African (AFR) AF: 0.169 AC: 7017 AN: 41448

American (AMR) AF: 0.520 AC: 7938 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.674 AC: 2341 AN: 3472

East Asian (EAS) AF: 0.556 AC: 2865 AN: 5154

South Asian (SAS) AF: 0.516 AC: 2487 AN: 4816

European-Finnish (FIN) AF: 0.697 AC: 7367 AN: 10570

Middle Eastern (MID) AF: 0.626 AC: 184 AN: 294

European-Non Finnish (NFE) AF: 0.652 AC: 44328 AN: 67962

Other (OTH) AF: 0.554 AC: 1168 AN: 2108

Alfa AF: 0.425 Hom.: 1535

Bravo AF: 0.478

Asia WGS AF: 0.538 AC: 1870 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.52
CADD	Benign	19
DANN	Benign	0.76
PhyloP100		0.99

Splicing

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

Other links and lift over

dbSNP: rs1516003; hg19: chr2-118334242;