10-78380416-C-T

Variant names:

• chr10-78380416-C-T
• rs11002528
• ENST00000421324.4:n.50+142112C>T

Variant summary

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

The ENST00000634452.1(LINC00595):​n.169C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0667 in 152,314 control chromosomes in the GnomAD database, including 410 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 0.067 (410 hom., cov: 32)
  • Exomes 𝑓: 0.16 (0 hom.)
• Consequence: LINC00595 ENST00000634452.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.337

Genes affected

ENSG00000282863 (HGNC:):

LINC00595 (HGNC:45111): (long intergenic non-protein coding RNA 856)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0919 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000282863	ENST00000421324.4	n.50+142112C>T		intron_variant	Intron 1 of 2	1
LINC00595	ENST00000634452.1	n.169C>T		non_coding_transcript_exon_variant	Exon 2 of 3	2
LINC00595	ENST00000635545.1	n.335C>T		non_coding_transcript_exon_variant	Exon 5 of 5	4

Frequencies

GnomAD3 genomes AF: 0.0667 AC: 10149 AN: 152134 Hom.: 408 Cov.: 32

Gnomad AFR AF: 0.0164

Gnomad AMI AF: 0.159

Gnomad AMR AF: 0.0671

Gnomad ASJ AF: 0.0571

Gnomad EAS AF: 0.0858

Gnomad SAS AF: 0.0524

Gnomad FIN AF: 0.0791

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0938

Gnomad OTH AF: 0.0746

GnomAD4 exome AF: 0.161 AC: 10 AN: 62 Hom.: 0 Cov.: 0 AF XY: 0.109 AC XY: 5 AN XY: 46

Gnomad4 AFR exome AF: 0.00

Gnomad4 EAS exome AF: 0.500

Gnomad4 SAS exome AF: 0.500

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.167

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.0667 AC: 10150 AN: 152252 Hom.: 410 Cov.: 32 AF XY: 0.0665 AC XY: 4950 AN XY: 74440

Gnomad4 AFR AF: 0.0164

Gnomad4 AMR AF: 0.0671

Gnomad4 ASJ AF: 0.0571

Gnomad4 EAS AF: 0.0864

Gnomad4 SAS AF: 0.0521

Gnomad4 FIN AF: 0.0791

Gnomad4 NFE AF: 0.0939

Gnomad4 OTH AF: 0.0753

Alfa AF: 0.0290 Hom.: 23

Bravo AF: 0.0651

Asia WGS AF: 0.0820 AC: 287 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	4.4
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: rs11002528; hg19: chr10-80140173;