rs8039031

Variant names:

• chr15-36874889-A-G
• rs8039031
• ENST00000690156.1:n.385+1471T>C

Variant summary

Our verdict is Benign. The variant received -9 ACMG points: 0P and 9B. BP4 BA1

The NR_024264.1(LOC145845):​n.687+1471T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.209 in 152,130 control chromosomes in the GnomAD database, including 3,601 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 0.21 (3601 hom., cov: 33)
• Consequence: LOC145845 NR_024264.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.42
• Publications: 6 publications found

Genes affected

ENSG00000259280 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -9 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.18).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.261 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_024264.1. 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
	LOC145845	NR_024264.1		n.687+1471T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000259280	ENST00000690156.1		n.385+1471T>C		intron	N/A
	ENSG00000259280	ENST00000785414.1		n.587+1471T>C		intron	N/A
	ENSG00000259280	ENST00000785415.1		n.613+4873T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.209 AC: 31725 AN: 152014 Hom.: 3600 Cov.: 33

Gnomad AFR AF: 0.265

Gnomad AMI AF: 0.228

Gnomad AMR AF: 0.147

Gnomad ASJ AF: 0.160

Gnomad EAS AF: 0.0405

Gnomad SAS AF: 0.182

Gnomad FIN AF: 0.174

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.211

Gnomad OTH AF: 0.183

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

GnomAD4 genome AF: 0.209 AC: 31741 AN: 152130 Hom.: 3601 Cov.: 33 AF XY: 0.203 AC XY: 15130 AN XY: 74396

African (AFR) AF: 0.265 AC: 10997 AN: 41484

American (AMR) AF: 0.147 AC: 2248 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.160 AC: 555 AN: 3472

East Asian (EAS) AF: 0.0406 AC: 211 AN: 5192

South Asian (SAS) AF: 0.182 AC: 880 AN: 4826

European-Finnish (FIN) AF: 0.174 AC: 1841 AN: 10604

Middle Eastern (MID) AF: 0.170 AC: 50 AN: 294

European-Non Finnish (NFE) AF: 0.211 AC: 14369 AN: 67950

Other (OTH) AF: 0.181 AC: 382 AN: 2108

Alfa AF: 0.205 Hom.: 1853

Bravo AF: 0.206

Asia WGS AF: 0.114 AC: 396 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.18
CADD	Benign	19
DANN	Benign	0.87
PhyloP100		3.4

Splicing

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

Other links and lift over

dbSNP: rs8039031; hg19: chr15-37167090;