rs10740479

Positions:

• chr10-78462711-G-A

Variant summary

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

The ENST00000421324.4(ENSG00000282863):​n.51-66040G>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 0.121 in 152,092 control chromosomes in the GnomAD database, including 1,310 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 0.12 (1310 hom., cov: 32)
• Consequence: ENST00000421324.4 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.981

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=-0.73).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.199 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.51-66040G>A		intron_variant, non_coding_transcript_variant		1
LINC00595	ENST00000635422.1	n.63-62619G>A		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.121 AC: 18424 AN: 151974 Hom.: 1305 Cov.: 32

Gnomad AFR AF: 0.0469

Gnomad AMI AF: 0.104

Gnomad AMR AF: 0.185

Gnomad ASJ AF: 0.136

Gnomad EAS AF: 0.210

Gnomad SAS AF: 0.113

Gnomad FIN AF: 0.135

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.144

Gnomad OTH AF: 0.121

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

GnomAD4 genome AF: 0.121 AC: 18437 AN: 152092 Hom.: 1310 Cov.: 32 AF XY: 0.122 AC XY: 9104 AN XY: 74356

Gnomad4 AFR AF: 0.0469

Gnomad4 AMR AF: 0.185

Gnomad4 ASJ AF: 0.136

Gnomad4 EAS AF: 0.210

Gnomad4 SAS AF: 0.113

Gnomad4 FIN AF: 0.135

Gnomad4 NFE AF: 0.144

Gnomad4 OTH AF: 0.122

Alfa AF: 0.135 Hom.: 357

Bravo AF: 0.120

Asia WGS AF: 0.157 AC: 548 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	6.8
DANN	Benign	0.95

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10740479; hg19: chr10-80222468;