10-89883850-C-T

Position:

• chr10-89883850-C-T

Variant summary

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

The NR_149080.1(LINC01374):​n.102+29843C>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 0.562 in 151,690 control chromosomes in the GnomAD database, including 25,447 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 0.56 (25447 hom., cov: 31)
• Consequence: LINC01374 NR_149080.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.207

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=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.747 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC01374	NR_149080.1	n.102+29843C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC01374	ENST00000664430.1	n.413+29843C>T		intron_variant, non_coding_transcript_variant
LINC01374	ENST00000629067.1	n.102+29843C>T		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.562 AC: 85168 AN: 151570 Hom.: 25386 Cov.: 31

Gnomad AFR AF: 0.754

Gnomad AMI AF: 0.486

Gnomad AMR AF: 0.610

Gnomad ASJ AF: 0.550

Gnomad EAS AF: 0.370

Gnomad SAS AF: 0.615

Gnomad FIN AF: 0.337

Gnomad MID AF: 0.576

Gnomad NFE AF: 0.482

Gnomad OTH AF: 0.567

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

GnomAD4 genome AF: 0.562 AC: 85299 AN: 151690 Hom.: 25447 Cov.: 31 AF XY: 0.557 AC XY: 41240 AN XY: 74096

Gnomad4 AFR AF: 0.754

Gnomad4 AMR AF: 0.610

Gnomad4 ASJ AF: 0.550

Gnomad4 EAS AF: 0.371

Gnomad4 SAS AF: 0.616

Gnomad4 FIN AF: 0.337

Gnomad4 NFE AF: 0.482

Gnomad4 OTH AF: 0.571

Alfa AF: 0.530 Hom.: 6885

Bravo AF: 0.588

Asia WGS AF: 0.556 AC: 1934 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	3.4
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1324705; hg19: chr10-91643607;