ENST00000586321.1:n.61-8642A>G

Variant names:

• chr17-78335323-A-G
• rs8076673
• ENST00000586321.1:n.61-8642A>G

Variant summary

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

The ENST00000586321.1(ENSG00000267737):​n.61-8642A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.18 in 151,992 control chromosomes in the GnomAD database, including 2,777 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 0.18 (2777 hom., cov: 32)
• Consequence: ENSG00000267737 ENST00000586321.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.599
• Publications: 1 publications found

Genes affected

ENSG00000267737 (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 (AFR) allele frequency at 95% confidence interval = 0.253 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105371912	NR_188632.1	n.74-8642A>G		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000267737	ENST00000586321.1	n.61-8642A>G		intron_variant	Intron 1 of 2	3
ENSG00000267737	ENST00000823930.1	n.39-8642A>G		intron_variant	Intron 1 of 1
ENSG00000267737	ENST00000823931.1	n.72-8642A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.180 AC: 27324 AN: 151874 Hom.: 2775 Cov.: 32

Gnomad AFR AF: 0.257

Gnomad AMI AF: 0.149

Gnomad AMR AF: 0.151

Gnomad ASJ AF: 0.181

Gnomad EAS AF: 0.00135

Gnomad SAS AF: 0.140

Gnomad FIN AF: 0.115

Gnomad MID AF: 0.121

Gnomad NFE AF: 0.167

Gnomad OTH AF: 0.161

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

GnomAD4 genome AF: 0.180 AC: 27341 AN: 151992 Hom.: 2777 Cov.: 32 AF XY: 0.174 AC XY: 12962 AN XY: 74290

African (AFR) AF: 0.257 AC: 10647 AN: 41428

American (AMR) AF: 0.151 AC: 2311 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.181 AC: 627 AN: 3468

East Asian (EAS) AF: 0.00135 AC: 7 AN: 5176

South Asian (SAS) AF: 0.140 AC: 673 AN: 4820

European-Finnish (FIN) AF: 0.115 AC: 1214 AN: 10576

Middle Eastern (MID) AF: 0.113 AC: 33 AN: 292

European-Non Finnish (NFE) AF: 0.167 AC: 11357 AN: 67942

Other (OTH) AF: 0.159 AC: 336 AN: 2110

Alfa AF: 0.198 Hom.: 1178

Bravo AF: 0.185

Asia WGS AF: 0.0700 AC: 247 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	1.7
DANN	Benign	0.71
PhyloP100		-0.60

Splicing

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

Other links and lift over

dbSNP: rs8076673; hg19: chr17-76331404;