2-118078449-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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107985940	XR_001739662.3	n.181+9802G>C		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000297418	ENST00000747789.1	n.231+9064G>C		intron_variant	Intron 2 of 4
ENSG00000297418	ENST00000747790.1	n.104+9802G>C		intron_variant	Intron 1 of 2
ENSG00000297418	ENST00000747791.1	n.272-3896G>C		intron_variant	Intron 2 of 4

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 v4.3

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;