chr2-118085861-T-C

Variant names:

• chr2-118085861-T-C
• rs17587352
• ENST00000747789.1:n.231+1652A>G

Variant summary

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

The ENST00000747789.1(ENSG00000297418):​n.231+1652A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0707 in 152,236 control chromosomes in the GnomAD database, including 531 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 0.071 (531 hom., cov: 33)
• Consequence: ENSG00000297418 ENST00000747789.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.326
• Publications: 5 publications found

Genes affected

ENSG00000297418 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.1 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000747789.1. 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
	ENSG00000297418	ENST00000747789.1		n.231+1652A>G		intron	N/A
	ENSG00000297418	ENST00000747790.1		n.104+2390A>G		intron	N/A
	ENSG00000297418	ENST00000747791.1		n.271+1652A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0706 AC: 10738 AN: 152118 Hom.: 527 Cov.: 33

Gnomad AFR AF: 0.0263

Gnomad AMI AF: 0.141

Gnomad AMR AF: 0.104

Gnomad ASJ AF: 0.0655

Gnomad EAS AF: 0.0408

Gnomad SAS AF: 0.0637

Gnomad FIN AF: 0.183

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.0750

Gnomad OTH AF: 0.0621

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

GnomAD4 genome AF: 0.0707 AC: 10760 AN: 152236 Hom.: 531 Cov.: 33 AF XY: 0.0762 AC XY: 5670 AN XY: 74412

African (AFR) AF: 0.0263 AC: 1091 AN: 41554

American (AMR) AF: 0.105 AC: 1600 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0655 AC: 227 AN: 3468

East Asian (EAS) AF: 0.0407 AC: 211 AN: 5186

South Asian (SAS) AF: 0.0637 AC: 307 AN: 4818

European-Finnish (FIN) AF: 0.183 AC: 1941 AN: 10592

Middle Eastern (MID) AF: 0.0272 AC: 8 AN: 294

European-Non Finnish (NFE) AF: 0.0750 AC: 5102 AN: 68008

Other (OTH) AF: 0.0681 AC: 144 AN: 2114

Alfa AF: 0.0706 Hom.: 711

Bravo AF: 0.0631

Asia WGS AF: 0.0640 AC: 222 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	11
DANN	Benign	0.82
PhyloP100		0.33

Splicing

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

Other links and lift over

dbSNP: rs17587352; hg19: chr2-118843437; COSMIC: COSV55522177;