chr10-78267509-G-A

Position:

• chr10-78267509-G-A

Variant summary

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

The NR_073447.2(LINC00595):​n.145+23G>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 0.319 in 152,008 control chromosomes in the GnomAD database, including 8,511 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 0.32 (8508 hom., cov: 33)
  • Exomes 𝑓: 0.39 (3 hom.)
• Consequence: LINC00595 NR_073447.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.213

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=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.665 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC00595	NR_073447.2	n.145+23G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000421324.4	n.50+29205G>A		intron_variant, non_coding_transcript_variant		1
LINC00595	ENST00000635422.1	n.62+88263G>A		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.319 AC: 48451 AN: 151856 Hom.: 8503 Cov.: 33

Gnomad AFR AF: 0.201

Gnomad AMI AF: 0.217

Gnomad AMR AF: 0.328

Gnomad ASJ AF: 0.330

Gnomad EAS AF: 0.684

Gnomad SAS AF: 0.428

Gnomad FIN AF: 0.471

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.331

Gnomad OTH AF: 0.296

GnomAD4 exome AF: 0.389 AC: 14 AN: 36 Hom.: 3 Cov.: 0 AF XY: 0.412 AC XY: 14 AN XY: 34

Gnomad4 AFR exome AF: 0.500

Gnomad4 ASJ exome AF: 0.00

Gnomad4 NFE exome AF: 0.462

Gnomad4 OTH exome AF: 0.250

GnomAD4 genome AF: 0.319 AC: 48483 AN: 151972 Hom.: 8508 Cov.: 33 AF XY: 0.330 AC XY: 24481 AN XY: 74254

Gnomad4 AFR AF: 0.201

Gnomad4 AMR AF: 0.328

Gnomad4 ASJ AF: 0.330

Gnomad4 EAS AF: 0.684

Gnomad4 SAS AF: 0.429

Gnomad4 FIN AF: 0.471

Gnomad4 NFE AF: 0.331

Gnomad4 OTH AF: 0.296

Alfa AF: 0.325 Hom.: 7675

Bravo AF: 0.303

Asia WGS AF: 0.523 AC: 1817 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.5
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1720293; hg19: chr10-80027266;