rs986222

chr10-90171130-G-A

Variant summary

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

The ENST00000664430.1(LINC01374):n.696-53909G>A 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 0.516 in 151,984 control chromosomes in the GnomAD database, including 21,146 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 0.52 (21146 hom., cov: 32)
• Consequence: LINC01374 ENST00000664430.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.326

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=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.94 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.696-53909G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.516 AC: 78293 AN: 151866 Hom.: 21123 Cov.: 32

Gnomad AFR AF: 0.507

Gnomad AMI AF: 0.338

Gnomad AMR AF: 0.547

Gnomad ASJ AF: 0.609

Gnomad EAS AF: 0.962

Gnomad SAS AF: 0.745

Gnomad FIN AF: 0.538

Gnomad MID AF: 0.595

Gnomad NFE AF: 0.457

Gnomad OTH AF: 0.512

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

GnomAD4 genome AF: 0.516 AC: 78355 AN: 151984 Hom.: 21146 Cov.: 32 AF XY: 0.527 AC XY: 39150 AN XY: 74280

Gnomad4 AFR AF: 0.507

Gnomad4 AMR AF: 0.547

Gnomad4 ASJ AF: 0.609

Gnomad4 EAS AF: 0.962

Gnomad4 SAS AF: 0.745

Gnomad4 FIN AF: 0.538

Gnomad4 NFE AF: 0.457

Gnomad4 OTH AF: 0.518

Alfa AF: 0.481 Hom.: 30049

Bravo AF: 0.512

Asia WGS AF: 0.826 AC: 2869 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	0.18
Dann	Benign	0.14

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs986222; hg19: chr10-91930887;