rs17047731

Variant names:

• chr2-118083157-G-A
• rs17047731
• ENST00000747789.1:n.231+4356C>T

Variant summary

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

The ENST00000747789.1(ENSG00000297418):​n.231+4356C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0876 in 152,056 control chromosomes in the GnomAD database, including 640 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 0.088 (640 hom., cov: 32)
• Consequence: ENSG00000297418 ENST00000747789.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.614
• Publications: 2 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=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.153 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000297418	ENST00000747789.1		n.231+4356C>T		intron	N/A
	ENSG00000297418	ENST00000747790.1		n.104+5094C>T		intron	N/A
	ENSG00000297418	ENST00000747791.1		n.271+4356C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0875 AC: 13291 AN: 151938 Hom.: 640 Cov.: 32

Gnomad AFR AF: 0.106

Gnomad AMI AF: 0.0901

Gnomad AMR AF: 0.0855

Gnomad ASJ AF: 0.0568

Gnomad EAS AF: 0.162

Gnomad SAS AF: 0.146

Gnomad FIN AF: 0.101

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.0665

Gnomad OTH AF: 0.0841

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

GnomAD4 genome AF: 0.0876 AC: 13315 AN: 152056 Hom.: 640 Cov.: 32 AF XY: 0.0897 AC XY: 6666 AN XY: 74314

African (AFR) AF: 0.106 AC: 4399 AN: 41482

American (AMR) AF: 0.0855 AC: 1305 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.0568 AC: 197 AN: 3470

East Asian (EAS) AF: 0.162 AC: 839 AN: 5170

South Asian (SAS) AF: 0.147 AC: 710 AN: 4818

European-Finnish (FIN) AF: 0.101 AC: 1066 AN: 10566

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

European-Non Finnish (NFE) AF: 0.0664 AC: 4516 AN: 67968

Other (OTH) AF: 0.0866 AC: 183 AN: 2114

Alfa AF: 0.0738 Hom.: 74

Bravo AF: 0.0833

Asia WGS AF: 0.166 AC: 574 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	4.8
DANN	Benign	0.68
PhyloP100		0.61

Splicing

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

Other links and lift over

dbSNP: rs17047731; hg19: chr2-118840733;