10-90051481-C-T

Position:

• chr10-90051481-C-T

Variant summary

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

The ENST00000664430.1(LINC01374):​n.549-48811C>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 0.0458 in 152,264 control chromosomes in the GnomAD database, including 320 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 0.046 (320 hom., cov: 33)
• Consequence: LINC01374 ENST00000664430.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.235

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=-0.77).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.171 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC01374	ENST00000664430.1	n.549-48811C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0458 AC: 6963 AN: 152146 Hom.: 320 Cov.: 33

Gnomad AFR AF: 0.0630

Gnomad AMI AF: 0.00879

Gnomad AMR AF: 0.0970

Gnomad ASJ AF: 0.0187

Gnomad EAS AF: 0.180

Gnomad SAS AF: 0.0785

Gnomad FIN AF: 0.0482

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.0130

Gnomad OTH AF: 0.0426

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

GnomAD4 genome AF: 0.0458 AC: 6974 AN: 152264 Hom.: 320 Cov.: 33 AF XY: 0.0498 AC XY: 3710 AN XY: 74450

Gnomad4 AFR AF: 0.0629

Gnomad4 AMR AF: 0.0971

Gnomad4 ASJ AF: 0.0187

Gnomad4 EAS AF: 0.181

Gnomad4 SAS AF: 0.0788

Gnomad4 FIN AF: 0.0482

Gnomad4 NFE AF: 0.0130

Gnomad4 OTH AF: 0.0422

Alfa AF: 0.0217 Hom.: 182

Bravo AF: 0.0483

Asia WGS AF: 0.117 AC: 406 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	7.5
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7097398; hg19: chr10-91811238;