rs17047697

Variant names:

• chr2-118070234-G-A
• rs17047697
• ENST00000747797.1:n.580C>T

Variant summary

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

The ENST00000747797.1(ENSG00000297418):​n.580C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.27 in 151,762 control chromosomes in the GnomAD database, including 6,114 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 0.27 (6114 hom., cov: 32)
• Consequence: ENSG00000297418 ENST00000747797.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.32
• Publications: 6 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=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.346 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000747797.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000297418	ENST00000747797.1		n.580C>T		non_coding_transcript_exon	Exon 4 of 4
	ENSG00000297418	ENST00000747789.1		n.231+17279C>T		intron	N/A
	ENSG00000297418	ENST00000747790.1		n.104+18017C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.271 AC: 41053 AN: 151644 Hom.: 6118 Cov.: 32

Gnomad AFR AF: 0.144

Gnomad AMI AF: 0.203

Gnomad AMR AF: 0.274

Gnomad ASJ AF: 0.353

Gnomad EAS AF: 0.359

Gnomad SAS AF: 0.293

Gnomad FIN AF: 0.339

Gnomad MID AF: 0.275

Gnomad NFE AF: 0.324

Gnomad OTH AF: 0.299

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

GnomAD4 genome AF: 0.270 AC: 41051 AN: 151762 Hom.: 6114 Cov.: 32 AF XY: 0.271 AC XY: 20128 AN XY: 74140

African (AFR) AF: 0.144 AC: 5967 AN: 41394

American (AMR) AF: 0.274 AC: 4162 AN: 15208

Ashkenazi Jewish (ASJ) AF: 0.353 AC: 1227 AN: 3472

East Asian (EAS) AF: 0.359 AC: 1846 AN: 5138

South Asian (SAS) AF: 0.293 AC: 1407 AN: 4806

European-Finnish (FIN) AF: 0.339 AC: 3562 AN: 10516

Middle Eastern (MID) AF: 0.272 AC: 80 AN: 294

European-Non Finnish (NFE) AF: 0.324 AC: 21989 AN: 67920

Other (OTH) AF: 0.297 AC: 627 AN: 2108

Alfa AF: 0.311 Hom.: 12295

Bravo AF: 0.263

Asia WGS AF: 0.316 AC: 1099 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	2.8
DANN	Benign	0.74
PhyloP100		-1.3

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs17047697;

hg19: chr2-118827810;