13-85091744-C-T

Variant names:

• chr13-85091744-C-T
• rs17079247
• ENST00000717725.1:n.140-12824G>A

Variant summary

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

The ENST00000717725.1(LINC00375):​n.140-12824G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.205 in 152,038 control chromosomes in the GnomAD database, including 3,914 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 0.20 (3914 hom., cov: 32)
• Consequence: LINC00375 ENST00000717725.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.339
• Publications: 8 publications found

Genes affected

LINC00375 (HGNC:42699): (long intergenic non-protein coding RNA 375)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.491 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC00375	NR_126383.1	n.31-12824G>A		intron_variant	Intron 1 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00375	ENST00000717725.1	n.140-12824G>A		intron_variant	Intron 2 of 6
LINC00375	ENST00000717726.1	n.103-12824G>A		intron_variant	Intron 1 of 5
LINC00375	ENST00000722540.1	n.190-12824G>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.205 AC: 31094 AN: 151920 Hom.: 3905 Cov.: 32

Gnomad AFR AF: 0.280

Gnomad AMI AF: 0.137

Gnomad AMR AF: 0.269

Gnomad ASJ AF: 0.105

Gnomad EAS AF: 0.508

Gnomad SAS AF: 0.169

Gnomad FIN AF: 0.216

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.129

Gnomad OTH AF: 0.183

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

GnomAD4 genome AF: 0.205 AC: 31135 AN: 152038 Hom.: 3914 Cov.: 32 AF XY: 0.209 AC XY: 15547 AN XY: 74318

African (AFR) AF: 0.280 AC: 11625 AN: 41470

American (AMR) AF: 0.270 AC: 4124 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.105 AC: 364 AN: 3470

East Asian (EAS) AF: 0.507 AC: 2602 AN: 5128

South Asian (SAS) AF: 0.169 AC: 813 AN: 4816

European-Finnish (FIN) AF: 0.216 AC: 2280 AN: 10580

Middle Eastern (MID) AF: 0.139 AC: 41 AN: 294

European-Non Finnish (NFE) AF: 0.129 AC: 8774 AN: 67994

Other (OTH) AF: 0.183 AC: 387 AN: 2110

Alfa AF: 0.170 Hom.: 4089

Bravo AF: 0.217

Asia WGS AF: 0.312 AC: 1085 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	14
DANN	Benign	0.54
PhyloP100		0.34

Splicing

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

Other links and lift over

dbSNP: rs17079247; hg19: chr13-85665879;