ENST00000586321.1:n.61-13506G>A

Variant names:

• chr17-78330459-G-A
• rs16971055
• ENST00000586321.1:n.61-13506G>A

Variant summary

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

The ENST00000586321.1(ENSG00000267737):​n.61-13506G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.088 in 150,598 control chromosomes in the GnomAD database, including 595 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 0.088 (595 hom., cov: 30)
• Consequence: ENSG00000267737 ENST00000586321.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.135
• Publications: 6 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=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.123 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000586321.1. 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
	LOC105371912	NR_188632.1		n.74-13506G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000267737	ENST00000586321.1	TSL:3	n.61-13506G>A		intron	N/A
	ENSG00000267737	ENST00000823930.1		n.39-13506G>A		intron	N/A
	ENSG00000267737	ENST00000823931.1		n.71+12471G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0881 AC: 13254 AN: 150512 Hom.: 597 Cov.: 30

Gnomad AFR AF: 0.108

Gnomad AMI AF: 0.0428

Gnomad AMR AF: 0.0605

Gnomad ASJ AF: 0.0983

Gnomad EAS AF: 0.00117

Gnomad SAS AF: 0.133

Gnomad FIN AF: 0.0625

Gnomad MID AF: 0.0860

Gnomad NFE AF: 0.0902

Gnomad OTH AF: 0.0796

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

GnomAD4 genome AF: 0.0880 AC: 13258 AN: 150598 Hom.: 595 Cov.: 30 AF XY: 0.0854 AC XY: 6279 AN XY: 73500

African (AFR) AF: 0.108 AC: 4393 AN: 40816

American (AMR) AF: 0.0603 AC: 912 AN: 15122

Ashkenazi Jewish (ASJ) AF: 0.0983 AC: 340 AN: 3458

East Asian (EAS) AF: 0.00117 AC: 6 AN: 5130

South Asian (SAS) AF: 0.131 AC: 625 AN: 4754

European-Finnish (FIN) AF: 0.0625 AC: 638 AN: 10214

Middle Eastern (MID) AF: 0.0816 AC: 24 AN: 294

European-Non Finnish (NFE) AF: 0.0902 AC: 6115 AN: 67824

Other (OTH) AF: 0.0800 AC: 166 AN: 2074

Alfa AF: 0.0902 Hom.: 1169

Bravo AF: 0.0874

Asia WGS AF: 0.0700 AC: 245 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.5
DANN	Benign	0.66
PhyloP100		0.14

Splicing

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

Other links and lift over

dbSNP: rs16971055; hg19: chr17-76326540;