2-10439098-G-C

Variant names:

• chr2-10439098-G-C
• rs818162
• ENST00000757451.1:n.252-4584G>C

Variant summary

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

The ENST00000757451.1(ENSG00000298698):​n.252-4584G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.733 in 152,184 control chromosomes in the GnomAD database, including 41,325 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 (41325 hom., cov: 33)
• Consequence: ENSG00000298698 ENST00000757451.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.390
• Publications: 1 publications found

Genes affected

ENSG00000298698 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.811 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000757451.1. 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
	ENSG00000298698	ENST00000757451.1		n.252-4584G>C		intron	N/A
	ENSG00000298698	ENST00000757452.1		n.133-2344G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.733 AC: 111435 AN: 152066 Hom.: 41305 Cov.: 33

Gnomad AFR AF: 0.795

Gnomad AMI AF: 0.754

Gnomad AMR AF: 0.665

Gnomad ASJ AF: 0.605

Gnomad EAS AF: 0.831

Gnomad SAS AF: 0.803

Gnomad FIN AF: 0.807

Gnomad MID AF: 0.604

Gnomad NFE AF: 0.695

Gnomad OTH AF: 0.680

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

GnomAD4 genome AF: 0.733 AC: 111504 AN: 152184 Hom.: 41325 Cov.: 33 AF XY: 0.739 AC XY: 54974 AN XY: 74424

African (AFR) AF: 0.794 AC: 32985 AN: 41518

American (AMR) AF: 0.665 AC: 10159 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.605 AC: 2098 AN: 3468

East Asian (EAS) AF: 0.832 AC: 4303 AN: 5174

South Asian (SAS) AF: 0.801 AC: 3862 AN: 4820

European-Finnish (FIN) AF: 0.807 AC: 8548 AN: 10594

Middle Eastern (MID) AF: 0.609 AC: 179 AN: 294

European-Non Finnish (NFE) AF: 0.695 AC: 47238 AN: 68006

Other (OTH) AF: 0.684 AC: 1444 AN: 2112

Alfa AF: 0.718 Hom.: 4865

Bravo AF: 0.725

Asia WGS AF: 0.809 AC: 2816 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.37
DANN	Benign	0.66
PhyloP100		-0.39

Splicing

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

Other links and lift over

dbSNP: rs818162; hg19: chr2-10579224;