rs10509593

Positions:

• chr10-90134005-G-A

Variant summary

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

The ENST00000664430.1(LINC01374):​n.695+33567G>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 0.0715 in 152,098 control chromosomes in the GnomAD database, including 638 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 0.071 (638 hom., cov: 32)
• Consequence: LINC01374 ENST00000664430.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.557

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 (EAS) allele frequency at 95% confidence interval = 0.194 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.695+33567G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0713 AC: 10843 AN: 151980 Hom.: 629 Cov.: 32

Gnomad AFR AF: 0.0894

Gnomad AMI AF: 0.00877

Gnomad AMR AF: 0.141

Gnomad ASJ AF: 0.0746

Gnomad EAS AF: 0.205

Gnomad SAS AF: 0.202

Gnomad FIN AF: 0.0519

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.0286

Gnomad OTH AF: 0.0821

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

GnomAD4 genome AF: 0.0715 AC: 10869 AN: 152098 Hom.: 638 Cov.: 32 AF XY: 0.0768 AC XY: 5709 AN XY: 74322

Gnomad4 AFR AF: 0.0894

Gnomad4 AMR AF: 0.141

Gnomad4 ASJ AF: 0.0746

Gnomad4 EAS AF: 0.204

Gnomad4 SAS AF: 0.202

Gnomad4 FIN AF: 0.0519

Gnomad4 NFE AF: 0.0286

Gnomad4 OTH AF: 0.0917

Alfa AF: 0.0473 Hom.: 32

Bravo AF: 0.0728

Asia WGS AF: 0.240 AC: 832 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.99
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10509593; hg19: chr10-91893762;