chr2-118078449-C-G

Variant names:

• chr2-118078449-C-G
• rs7566605
• ENST00000747789.1:n.231+9064G>C

Variant summary

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

The ENST00000747789.1(ENSG00000297418):​n.231+9064G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.702 in 152,038 control chromosomes in the GnomAD database, including 37,662 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 0.70 (37662 hom., cov: 31)
• Consequence: ENSG00000297418 ENST00000747789.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.89
• Publications: 137 publications found

Genes affected

ENSG00000297418 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.31).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.753 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+9064G>C		intron	N/A
	ENSG00000297418	ENST00000747790.1		n.104+9802G>C		intron	N/A
	ENSG00000297418	ENST00000747791.1		n.272-3896G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.702 AC: 106620 AN: 151920 Hom.: 37626 Cov.: 31

Gnomad AFR AF: 0.760

Gnomad AMI AF: 0.795

Gnomad AMR AF: 0.716

Gnomad ASJ AF: 0.646

Gnomad EAS AF: 0.640

Gnomad SAS AF: 0.706

Gnomad FIN AF: 0.662

Gnomad MID AF: 0.718

Gnomad NFE AF: 0.676

Gnomad OTH AF: 0.685

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

GnomAD4 genome AF: 0.702 AC: 106712 AN: 152038 Hom.: 37662 Cov.: 31 AF XY: 0.702 AC XY: 52150 AN XY: 74320

African (AFR) AF: 0.760 AC: 31494 AN: 41458

American (AMR) AF: 0.716 AC: 10942 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.646 AC: 2243 AN: 3470

East Asian (EAS) AF: 0.640 AC: 3312 AN: 5176

South Asian (SAS) AF: 0.706 AC: 3408 AN: 4824

European-Finnish (FIN) AF: 0.662 AC: 6994 AN: 10558

Middle Eastern (MID) AF: 0.721 AC: 212 AN: 294

European-Non Finnish (NFE) AF: 0.676 AC: 45936 AN: 67968

Other (OTH) AF: 0.687 AC: 1446 AN: 2106

Alfa AF: 0.703 Hom.: 4673

Bravo AF: 0.705

Asia WGS AF: 0.676 AC: 2351 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.31
CADD	Benign	16
DANN	Benign	0.67
PhyloP100		1.9

Splicing

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

Other links and lift over

dbSNP: rs7566605; hg19: chr2-118836025; COSMIC: COSV60100130;