rs17047718

Variant names:

• chr2-118079736-A-G
• rs17047718
• ENST00000747789.1:n.231+7777T>C

Variant summary

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

The ENST00000747789.1(ENSG00000297418):​n.231+7777T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0678 in 152,310 control chromosomes in the GnomAD database, including 434 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 0.068 (434 hom., cov: 32)
• Consequence: ENSG00000297418 ENST00000747789.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.940
• Publications: 4 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=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.159 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107985940	XR_001739662.3	n.181+8515T>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+7777T>C		intron_variant	Intron 2 of 4
ENSG00000297418	ENST00000747790.1	n.104+8515T>C		intron_variant	Intron 1 of 2
ENSG00000297418	ENST00000747791.1	n.272-5183T>C		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes AF: 0.0678 AC: 10322 AN: 152192 Hom.: 434 Cov.: 32

Gnomad AFR AF: 0.0425

Gnomad AMI AF: 0.110

Gnomad AMR AF: 0.0722

Gnomad ASJ AF: 0.0542

Gnomad EAS AF: 0.167

Gnomad SAS AF: 0.147

Gnomad FIN AF: 0.0992

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.0642

Gnomad OTH AF: 0.0712

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

GnomAD4 genome AF: 0.0678 AC: 10333 AN: 152310 Hom.: 434 Cov.: 32 AF XY: 0.0705 AC XY: 5251 AN XY: 74482

African (AFR) AF: 0.0425 AC: 1766 AN: 41574

American (AMR) AF: 0.0722 AC: 1104 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0542 AC: 188 AN: 3470

East Asian (EAS) AF: 0.168 AC: 869 AN: 5178

South Asian (SAS) AF: 0.148 AC: 714 AN: 4826

European-Finnish (FIN) AF: 0.0992 AC: 1053 AN: 10618

Middle Eastern (MID) AF: 0.0612 AC: 18 AN: 294

European-Non Finnish (NFE) AF: 0.0642 AC: 4365 AN: 68024

Other (OTH) AF: 0.0737 AC: 156 AN: 2116

Alfa AF: 0.0549 Hom.: 39

Bravo AF: 0.0626

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	5.4
DANN	Benign	0.67
PhyloP100		0.94

Splicing

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

Other links and lift over

dbSNP: rs17047718; hg19: chr2-118837312;