rs1076039

Variant names:

• chr17-4622476-A-T
• rs1076039
• ENST00000820607.1:n.389+5187T>A

Variant summary

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

The ENST00000820607.1(ENSG00000306739):​n.389+5187T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.107 in 152,116 control chromosomes in the GnomAD database, including 1,102 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 0.11 (1102 hom., cov: 32)
• Consequence: ENSG00000306739 ENST00000820607.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0670
• Publications: 1 publications found

Genes affected

ENSG00000306739 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.151 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000820607.1. 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
	ENSG00000306739	ENST00000820607.1		n.389+5187T>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.107 AC: 16211 AN: 151998 Hom.: 1102 Cov.: 32

Gnomad AFR AF: 0.0292

Gnomad AMI AF: 0.181

Gnomad AMR AF: 0.139

Gnomad ASJ AF: 0.126

Gnomad EAS AF: 0.00173

Gnomad SAS AF: 0.0466

Gnomad FIN AF: 0.122

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.154

Gnomad OTH AF: 0.125

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

GnomAD4 genome AF: 0.107 AC: 16213 AN: 152116 Hom.: 1102 Cov.: 32 AF XY: 0.104 AC XY: 7770 AN XY: 74366

African (AFR) AF: 0.0291 AC: 1206 AN: 41492

American (AMR) AF: 0.140 AC: 2133 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.126 AC: 437 AN: 3470

East Asian (EAS) AF: 0.00174 AC: 9 AN: 5176

South Asian (SAS) AF: 0.0465 AC: 224 AN: 4822

European-Finnish (FIN) AF: 0.122 AC: 1289 AN: 10582

Middle Eastern (MID) AF: 0.160 AC: 47 AN: 294

European-Non Finnish (NFE) AF: 0.154 AC: 10442 AN: 67982

Other (OTH) AF: 0.124 AC: 261 AN: 2110

Alfa AF: 0.125 Hom.: 162

Bravo AF: 0.104

Asia WGS AF: 0.0250 AC: 89 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	1.9
DANN	Benign	0.89
PhyloP100		0.067

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: rs1076039;

hg19: chr17-4525771;