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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107985940	XR_001739662.3	n.182-7218C>T		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000297418	ENST00000747797.1	n.580C>T		non_coding_transcript_exon_variant	Exon 4 of 4
ENSG00000297418	ENST00000747789.1	n.231+17279C>T		intron_variant	Intron 2 of 4
ENSG00000297418	ENST00000747790.1	n.104+18017C>T		intron_variant	Intron 1 of 2

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 v4.3

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

Other links and lift over

dbSNP: rs17047697; hg19: chr2-118827810;