rs17173656

Variant names:

• chr7-150901571-T-C
• rs17173656
• ENST00000726373.1:n.45A>G

Your query was ambiguous. Multiple possible variants found:

• chr7-150901571-T-C
• chr7-150901571-T-G

Variant summary

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

The ENST00000726373.1(ENSG00000289052):​n.45A>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 0.127 in 152,064 control chromosomes in the GnomAD database, including 1,434 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 0.13 (1434 hom., cov: 32)
• Consequence: ENSG00000289052 ENST00000726373.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0550
• Publications: 5 publications found

Genes affected

ENSG00000289052 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.297 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000289052	ENST00000726373.1	n.45A>G		non_coding_transcript_exon_variant	Exon 1 of 2
ENSG00000289052	ENST00000726378.1	n.69A>G		non_coding_transcript_exon_variant	Exon 1 of 2

Frequencies

GnomAD3 genomes AF: 0.127 AC: 19343 AN: 151946 Hom.: 1433 Cov.: 32

Gnomad AFR AF: 0.129

Gnomad AMI AF: 0.150

Gnomad AMR AF: 0.189

Gnomad ASJ AF: 0.120

Gnomad EAS AF: 0.310

Gnomad SAS AF: 0.139

Gnomad FIN AF: 0.151

Gnomad MID AF: 0.182

Gnomad NFE AF: 0.0937

Gnomad OTH AF: 0.136

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

GnomAD4 genome AF: 0.127 AC: 19375 AN: 152064 Hom.: 1434 Cov.: 32 AF XY: 0.133 AC XY: 9907 AN XY: 74318

African (AFR) AF: 0.129 AC: 5344 AN: 41496

American (AMR) AF: 0.189 AC: 2893 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.120 AC: 415 AN: 3460

East Asian (EAS) AF: 0.309 AC: 1596 AN: 5158

South Asian (SAS) AF: 0.140 AC: 674 AN: 4814

European-Finnish (FIN) AF: 0.151 AC: 1596 AN: 10560

Middle Eastern (MID) AF: 0.182 AC: 53 AN: 292

European-Non Finnish (NFE) AF: 0.0937 AC: 6371 AN: 67966

Other (OTH) AF: 0.140 AC: 296 AN: 2112

Alfa AF: 0.106 Hom.: 2346

Bravo AF: 0.133

Asia WGS AF: 0.227 AC: 790 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.6
DANN	Benign	0.79
PhyloP100		-0.055

Splicing

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

Other links and lift over

dbSNP: rs17173656; hg19: chr7-150598659;