17-42457387-A-G

Variant names:

• chr17-42457387-A-G
• rs9897702
• ENST00000723361.1:n.642A>G

Variant summary

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

The ENST00000723361.1(ENSG00000294400):​n.642A>G 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 0.705 in 151,990 control chromosomes in the GnomAD database, including 38,304 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 (38304 hom., cov: 31)
• Consequence: ENSG00000294400 ENST00000723361.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.159
• Publications: 15 publications found

Genes affected

ENSG00000294400 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.954 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000723361.1. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000294400	ENST00000723361.1		n.642A>G		non_coding_transcript_exon	Exon 1 of 1
	ENSG00000294400	ENST00000723360.1		n.*185A>G		downstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.705 AC: 107051 AN: 151872 Hom.: 38254 Cov.: 31

Gnomad AFR AF: 0.605

Gnomad AMI AF: 0.811

Gnomad AMR AF: 0.728

Gnomad ASJ AF: 0.807

Gnomad EAS AF: 0.976

Gnomad SAS AF: 0.843

Gnomad FIN AF: 0.704

Gnomad MID AF: 0.842

Gnomad NFE AF: 0.720

Gnomad OTH AF: 0.770

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

GnomAD4 genome AF: 0.705 AC: 107152 AN: 151990 Hom.: 38304 Cov.: 31 AF XY: 0.711 AC XY: 52782 AN XY: 74268

African (AFR) AF: 0.606 AC: 25111 AN: 41416

American (AMR) AF: 0.727 AC: 11099 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.807 AC: 2803 AN: 3472

East Asian (EAS) AF: 0.976 AC: 5067 AN: 5190

South Asian (SAS) AF: 0.843 AC: 4060 AN: 4814

European-Finnish (FIN) AF: 0.704 AC: 7425 AN: 10546

Middle Eastern (MID) AF: 0.850 AC: 250 AN: 294

European-Non Finnish (NFE) AF: 0.720 AC: 48972 AN: 67986

Other (OTH) AF: 0.774 AC: 1629 AN: 2106

Alfa AF: 0.727 Hom.: 74417

Bravo AF: 0.700

Asia WGS AF: 0.893 AC: 3104 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	3.2
DANN	Benign	0.33
PhyloP100		0.16

Splicing

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

Other links and lift over

dbSNP: rs9897702; hg19: chr17-40609405;