rs17691129

Variant names:

• chr7-91538287-A-G
• rs17691129
• ENST00000718158.1:n.245T>C

Your query was ambiguous. Multiple possible variants found:

• chr7-91538287-A-G
• chr7-91538287-A-T

Variant summary

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

The ENST00000718158.1(ENSG00000223665):​n.245T>C 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 0.17 in 152,196 control chromosomes in the GnomAD database, including 2,494 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 0.17 (2494 hom., cov: 32)
• Consequence: ENSG00000223665 ENST00000718158.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.730
• Publications: 1 publications found

Genes affected

ENSG00000223665 (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 (NFE) allele frequency at 95% confidence interval = 0.211 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000718158.1. 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
	ENSG00000223665	ENST00000718158.1		n.245T>C		non_coding_transcript_exon	Exon 2 of 7
	ENSG00000223665	ENST00000840183.1		n.47T>C		non_coding_transcript_exon	Exon 1 of 8
	ENSG00000223665	ENST00000840184.1		n.47T>C		non_coding_transcript_exon	Exon 1 of 5

Frequencies

GnomAD3 genomes AF: 0.170 AC: 25812 AN: 152078 Hom.: 2490 Cov.: 32

Gnomad AFR AF: 0.0983

Gnomad AMI AF: 0.132

Gnomad AMR AF: 0.162

Gnomad ASJ AF: 0.276

Gnomad EAS AF: 0.0635

Gnomad SAS AF: 0.167

Gnomad FIN AF: 0.192

Gnomad MID AF: 0.266

Gnomad NFE AF: 0.214

Gnomad OTH AF: 0.188

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

GnomAD4 genome AF: 0.170 AC: 25818 AN: 152196 Hom.: 2494 Cov.: 32 AF XY: 0.168 AC XY: 12467 AN XY: 74404

African (AFR) AF: 0.0983 AC: 4083 AN: 41542

American (AMR) AF: 0.162 AC: 2474 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.276 AC: 959 AN: 3470

East Asian (EAS) AF: 0.0634 AC: 328 AN: 5172

South Asian (SAS) AF: 0.168 AC: 811 AN: 4822

European-Finnish (FIN) AF: 0.192 AC: 2028 AN: 10580

Middle Eastern (MID) AF: 0.259 AC: 76 AN: 294

European-Non Finnish (NFE) AF: 0.214 AC: 14549 AN: 68002

Other (OTH) AF: 0.185 AC: 390 AN: 2106

Alfa AF: 0.204 Hom.: 5640

Bravo AF: 0.166

Asia WGS AF: 0.0980 AC: 341 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.41
DANN	Benign	0.45
PhyloP100		-0.73

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: rs17691129;

hg19: chr7-91167602;