10-78380416-C-T

Position:

• chr10-78380416-C-T

Variant summary

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

The ENST00000421324.4(ENSG00000282863):​n.50+142112C>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 0.0667 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: ENST00000421324.4 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.337

Genes affected

(HGNC:):

LINC00595 (HGNC:31430): (long intergenic non-protein coding RNA 595)

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000421324.4	n.50+142112C>T		intron_variant, non_coding_transcript_variant		1
LINC00595	ENST00000635422.1	n.63-144914C>T		intron_variant, non_coding_transcript_variant		5

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;