rs10509586

chr10-89981680-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000664430.1(LINC01374):n.548+66910G>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0679 in 152,244 control chromosomes in the GnomAD database, including 616 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 0.068 (616 hom., cov: 32)
• Consequence: LINC01374 ENST00000664430.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.560

Genes affected

LINC01374 (HGNC:50631): (long intergenic non-protein coding RNA 1374)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.148 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01374	ENST00000664430.1	n.548+66910G>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0679 AC: 10327 AN: 152126 Hom.: 618 Cov.: 32

Gnomad AFR AF: 0.152

Gnomad AMI AF: 0.0833

Gnomad AMR AF: 0.0349

Gnomad ASJ AF: 0.0476

Gnomad EAS AF: 0.00327

Gnomad SAS AF: 0.0114

Gnomad FIN AF: 0.0129

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0433

Gnomad OTH AF: 0.0531

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

GnomAD4 genome AF: 0.0679 AC: 10333 AN: 152244 Hom.: 616 Cov.: 32 AF XY: 0.0639 AC XY: 4754 AN XY: 74446

Gnomad4 AFR AF: 0.151

Gnomad4 AMR AF: 0.0349

Gnomad4 ASJ AF: 0.0476

Gnomad4 EAS AF: 0.00347

Gnomad4 SAS AF: 0.0116

Gnomad4 FIN AF: 0.0129

Gnomad4 NFE AF: 0.0432

Gnomad4 OTH AF: 0.0521

Alfa AF: 0.0477 Hom.: 91

Bravo AF: 0.0740

Asia WGS AF: 0.0150 AC: 52 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	0.11
Dann	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10509586; hg19: chr10-91741437;