9-79870718-C-T

Variant names:

• chr9-79870718-C-T
• rs3894377
• ENST00000703218.1:n.598-3850G>A

Variant summary

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

The ENST00000703218.1(ENSG00000232494):​n.598-3850G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.523 in 151,298 control chromosomes in the GnomAD database, including 20,684 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 0.52 (20684 hom., cov: 31)
• Consequence: ENSG00000232494 ENST00000703218.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.285
• Publications: 4 publications found

Genes affected

ENSG00000232494 (HGNC:):

LINC01507 (HGNC:51189): (long intergenic non-protein coding RNA 1507)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.598 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01507	NR_121213.1	n.97+46092C>T		intron_variant	Intron 1 of 2
LOC105376101	XR_001746762.1	n.143+3772G>A		intron_variant	Intron 2 of 3
LOC105376101	XR_001746763.1	n.655-3850G>A		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000232494	ENST00000703218.1	n.598-3850G>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.523 AC: 79048 AN: 151180 Hom.: 20682 Cov.: 31

Gnomad AFR AF: 0.534

Gnomad AMI AF: 0.518

Gnomad AMR AF: 0.470

Gnomad ASJ AF: 0.527

Gnomad EAS AF: 0.616

Gnomad SAS AF: 0.541

Gnomad FIN AF: 0.535

Gnomad MID AF: 0.516

Gnomad NFE AF: 0.518

Gnomad OTH AF: 0.525

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

GnomAD4 genome AF: 0.523 AC: 79077 AN: 151298 Hom.: 20684 Cov.: 31 AF XY: 0.524 AC XY: 38665 AN XY: 73850

African (AFR) AF: 0.533 AC: 21974 AN: 41216

American (AMR) AF: 0.470 AC: 7159 AN: 15234

Ashkenazi Jewish (ASJ) AF: 0.527 AC: 1824 AN: 3464

East Asian (EAS) AF: 0.616 AC: 3153 AN: 5122

South Asian (SAS) AF: 0.542 AC: 2587 AN: 4772

European-Finnish (FIN) AF: 0.535 AC: 5566 AN: 10396

Middle Eastern (MID) AF: 0.524 AC: 154 AN: 294

European-Non Finnish (NFE) AF: 0.518 AC: 35097 AN: 67792

Other (OTH) AF: 0.520 AC: 1094 AN: 2102

Alfa AF: 0.519 Hom.: 89471

Bravo AF: 0.519

Asia WGS AF: 0.530 AC: 1821 AN: 3436

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	5.1
DANN	Benign	0.78
PhyloP100		0.28

Splicing

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

Other links and lift over

dbSNP: rs3894377; hg19: chr9-82485633;