2-76495179-T-C

Variant names:

• chr2-76495179-T-C
• rs17012789
• ENST00000798785.1:n.283-8998T>C

Variant summary

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

The ENST00000798785.1(ENSG00000287172):​n.283-8998T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.162 in 151,854 control chromosomes in the GnomAD database, including 2,690 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 (2690 hom., cov: 32)
• Consequence: ENSG00000287172 ENST00000798785.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.737
• Publications: 3 publications found

Genes affected

ENSG00000287172 (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 (EAS) allele frequency at 95% confidence interval = 0.49 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000798785.1. 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
	ENSG00000287172	ENST00000798785.1		n.283-8998T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.162 AC: 24653 AN: 151736 Hom.: 2694 Cov.: 32

Gnomad AFR AF: 0.0537

Gnomad AMI AF: 0.150

Gnomad AMR AF: 0.218

Gnomad ASJ AF: 0.223

Gnomad EAS AF: 0.507

Gnomad SAS AF: 0.290

Gnomad FIN AF: 0.126

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.183

Gnomad OTH AF: 0.180

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

GnomAD4 genome AF: 0.162 AC: 24656 AN: 151854 Hom.: 2690 Cov.: 32 AF XY: 0.165 AC XY: 12259 AN XY: 74192

African (AFR) AF: 0.0535 AC: 2219 AN: 41448

American (AMR) AF: 0.218 AC: 3323 AN: 15232

Ashkenazi Jewish (ASJ) AF: 0.223 AC: 774 AN: 3468

East Asian (EAS) AF: 0.506 AC: 2594 AN: 5124

South Asian (SAS) AF: 0.291 AC: 1396 AN: 4804

European-Finnish (FIN) AF: 0.126 AC: 1333 AN: 10564

Middle Eastern (MID) AF: 0.248 AC: 73 AN: 294

European-Non Finnish (NFE) AF: 0.183 AC: 12421 AN: 67902

Other (OTH) AF: 0.183 AC: 387 AN: 2110

Alfa AF: 0.182 Hom.: 1433

Bravo AF: 0.166

Asia WGS AF: 0.374 AC: 1297 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.6
DANN	Benign	0.48
PhyloP100		-0.74

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs17012789;

hg19: chr2-76722305;