ENST00000658032.1:n.331-18014T>C

Variant names:

• chr7-110383304-A-G
• rs17157642
• ENST00000658032.1:n.331-18014T>C

Variant summary

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

The ENST00000658032.1(ENSG00000226965):​n.331-18014T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.146 in 152,212 control chromosomes in the GnomAD database, including 1,772 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 0.15 (1772 hom., cov: 32)
• Consequence: ENSG00000226965 ENST00000658032.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0100
• Publications: 3 publications found

Genes affected

ENSG00000226965 (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 (SAS) allele frequency at 95% confidence interval = 0.241 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105375451	XR_927863.3	n.387-18014T>C		intron_variant	Intron 4 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000226965	ENST00000658032.1	n.331-18014T>C		intron_variant	Intron 3 of 5
ENSG00000226965	ENST00000666128.1	n.98-18014T>C		intron_variant	Intron 2 of 3
ENSG00000226965	ENST00000667232.1	n.412-18014T>C		intron_variant	Intron 4 of 7
ENSG00000226965	ENST00000843035.1	n.352-18014T>C		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.146 AC: 22159 AN: 152094 Hom.: 1770 Cov.: 32

Gnomad AFR AF: 0.0920

Gnomad AMI AF: 0.260

Gnomad AMR AF: 0.114

Gnomad ASJ AF: 0.174

Gnomad EAS AF: 0.142

Gnomad SAS AF: 0.254

Gnomad FIN AF: 0.167

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.171

Gnomad OTH AF: 0.165

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

GnomAD4 genome AF: 0.146 AC: 22170 AN: 152212 Hom.: 1772 Cov.: 32 AF XY: 0.149 AC XY: 11087 AN XY: 74414

African (AFR) AF: 0.0920 AC: 3824 AN: 41544

American (AMR) AF: 0.114 AC: 1741 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.174 AC: 604 AN: 3472

East Asian (EAS) AF: 0.142 AC: 733 AN: 5172

South Asian (SAS) AF: 0.253 AC: 1222 AN: 4830

European-Finnish (FIN) AF: 0.167 AC: 1769 AN: 10584

Middle Eastern (MID) AF: 0.221 AC: 65 AN: 294

European-Non Finnish (NFE) AF: 0.171 AC: 11617 AN: 68006

Other (OTH) AF: 0.170 AC: 358 AN: 2112

Alfa AF: 0.151 Hom.: 296

Bravo AF: 0.135

Asia WGS AF: 0.228 AC: 791 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	1.5
DANN	Benign	0.73
PhyloP100		0.010

Splicing

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

Other links and lift over

dbSNP: rs17157642; hg19: chr7-110023361;