ENST00000691159.1:n.319-1294C>T

Variant names:

• chr6-170187139-G-A
• rs9459971
• ENST00000691159.1:n.319-1294C>T

Variant summary

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

The ENST00000691159.1(ENSG00000230960):​n.319-1294C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.679 in 151,568 control chromosomes in the GnomAD database, including 36,588 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 0.68 (36588 hom., cov: 28)
• Consequence: ENSG00000230960 ENST00000691159.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.133
• Publications: 5 publications found

Genes affected

ENSG00000230960 (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 (SAS) allele frequency at 95% confidence interval = 0.808 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
ENSG00000230960	ENST00000691159.1	n.319-1294C>T		intron_variant	Intron 1 of 2
ENSG00000230960	ENST00000701993.1	n.275-1294C>T		intron_variant	Intron 1 of 2
ENSG00000230960	ENST00000843770.1	n.437-1294C>T		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.680 AC: 102916 AN: 151450 Hom.: 36558 Cov.: 28

Gnomad AFR AF: 0.452

Gnomad AMI AF: 0.712

Gnomad AMR AF: 0.748

Gnomad ASJ AF: 0.723

Gnomad EAS AF: 0.749

Gnomad SAS AF: 0.830

Gnomad FIN AF: 0.781

Gnomad MID AF: 0.592

Gnomad NFE AF: 0.768

Gnomad OTH AF: 0.692

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

GnomAD4 genome AF: 0.679 AC: 102986 AN: 151568 Hom.: 36588 Cov.: 28 AF XY: 0.683 AC XY: 50567 AN XY: 74052

African (AFR) AF: 0.452 AC: 18625 AN: 41248

American (AMR) AF: 0.749 AC: 11443 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.723 AC: 2509 AN: 3472

East Asian (EAS) AF: 0.750 AC: 3806 AN: 5076

South Asian (SAS) AF: 0.830 AC: 3967 AN: 4780

European-Finnish (FIN) AF: 0.781 AC: 8245 AN: 10552

Middle Eastern (MID) AF: 0.596 AC: 174 AN: 292

European-Non Finnish (NFE) AF: 0.768 AC: 52111 AN: 67860

Other (OTH) AF: 0.694 AC: 1457 AN: 2098

Alfa AF: 0.743 Hom.: 77213

Bravo AF: 0.661

Asia WGS AF: 0.771 AC: 2681 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.2
DANN	Benign	0.73
PhyloP100		-0.13

Splicing

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

Other links and lift over

dbSNP: rs9459971; hg19: chr6-170502363;