rs6108701

Variant names:

• chr20-10785514-C-T
• rs6108701
• XR_001754497.2:n.8575C>T

Variant summary

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

The XR_001754497.2(LOC107985398):​n.8575C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.445 in 152,026 control chromosomes in the GnomAD database, including 15,545 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 0.44 (15545 hom., cov: 32)
• Consequence: LOC107985398 XR_001754497.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.427
• Publications: 2 publications found

Genes affected

LOC107985398 (HGNC:):

LINC01752 (HGNC:52540): (long intergenic non-protein coding RNA 1752)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.489 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107985398	XR_001754497.2	n.8575C>T		non_coding_transcript_exon_variant	Exon 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000270792	ENST00000605292.5	n.98+112489C>T		intron_variant	Intron 1 of 4	3
LINC01752	ENST00000667822.1	n.331+112489C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.445 AC: 67554 AN: 151908 Hom.: 15531 Cov.: 32

Gnomad AFR AF: 0.386

Gnomad AMI AF: 0.403

Gnomad AMR AF: 0.347

Gnomad ASJ AF: 0.497

Gnomad EAS AF: 0.316

Gnomad SAS AF: 0.425

Gnomad FIN AF: 0.564

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.494

Gnomad OTH AF: 0.414

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

GnomAD4 genome AF: 0.445 AC: 67591 AN: 152026 Hom.: 15545 Cov.: 32 AF XY: 0.444 AC XY: 33017 AN XY: 74318

African (AFR) AF: 0.386 AC: 16016 AN: 41470

American (AMR) AF: 0.347 AC: 5300 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.497 AC: 1724 AN: 3472

East Asian (EAS) AF: 0.315 AC: 1624 AN: 5158

South Asian (SAS) AF: 0.424 AC: 2045 AN: 4822

European-Finnish (FIN) AF: 0.564 AC: 5963 AN: 10566

Middle Eastern (MID) AF: 0.429 AC: 126 AN: 294

European-Non Finnish (NFE) AF: 0.494 AC: 33558 AN: 67946

Other (OTH) AF: 0.411 AC: 868 AN: 2110

Alfa AF: 0.467 Hom.: 13550

Bravo AF: 0.421

Asia WGS AF: 0.390 AC: 1359 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.49
DANN	Benign	0.20
PhyloP100		-0.43

Splicing

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

Other links and lift over

dbSNP: rs6108701; hg19: chr20-10766162;