rs2019080

chr10-78521979-G-A

Variant summary

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

The ENST00000421324.4(ENSG00000282863):n.51-6772G>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 0.494 in 151,910 control chromosomes in the GnomAD database, including 19,206 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 0.49 (19206 hom., cov: 32)
• Consequence: ENST00000421324.4 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.518

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=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.548 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
	ENST00000421324.4	n.51-6772G>A		intron_variant, non_coding_transcript_variant		1
LINC00595	ENST00000635422.1	n.63-3351G>A		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.494 AC: 74984 AN: 151792 Hom.: 19200 Cov.: 32

Gnomad AFR AF: 0.460

Gnomad AMI AF: 0.565

Gnomad AMR AF: 0.483

Gnomad ASJ AF: 0.452

Gnomad EAS AF: 0.0379

Gnomad SAS AF: 0.368

Gnomad FIN AF: 0.560

Gnomad MID AF: 0.465

Gnomad NFE AF: 0.552

Gnomad OTH AF: 0.485

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

GnomAD4 genome AF: 0.494 AC: 75012 AN: 151910 Hom.: 19206 Cov.: 32 AF XY: 0.488 AC XY: 36217 AN XY: 74236

Gnomad4 AFR AF: 0.459

Gnomad4 AMR AF: 0.483

Gnomad4 ASJ AF: 0.452

Gnomad4 EAS AF: 0.0381

Gnomad4 SAS AF: 0.369

Gnomad4 FIN AF: 0.560

Gnomad4 NFE AF: 0.552

Gnomad4 OTH AF: 0.479

Alfa AF: 0.505 Hom.: 3305

Bravo AF: 0.487

Asia WGS AF: 0.227 AC: 792 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
Cadd	Benign	3.3
Dann	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2019080; hg19: chr10-80281736;