rs1369752

Positions:

• chr10-78488998-T-C

Variant summary

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

The ENST00000421324.4(ENSG00000282863):​n.51-39753T>C 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 0.314 in 152,126 control chromosomes in the GnomAD database, including 9,155 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 0.31 (9155 hom., cov: 33)
• Consequence: ENST00000421324.4 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.12

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=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.535 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.51-39753T>C		intron_variant, non_coding_transcript_variant		1
LINC00595	ENST00000635422.1	n.63-36332T>C		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.314 AC: 47736 AN: 152006 Hom.: 9117 Cov.: 33

Gnomad AFR AF: 0.540

Gnomad AMI AF: 0.132

Gnomad AMR AF: 0.297

Gnomad ASJ AF: 0.370

Gnomad EAS AF: 0.288

Gnomad SAS AF: 0.366

Gnomad FIN AF: 0.173

Gnomad MID AF: 0.294

Gnomad NFE AF: 0.200

Gnomad OTH AF: 0.314

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

GnomAD4 genome AF: 0.314 AC: 47823 AN: 152126 Hom.: 9155 Cov.: 33 AF XY: 0.314 AC XY: 23355 AN XY: 74362

Gnomad4 AFR AF: 0.541

Gnomad4 AMR AF: 0.297

Gnomad4 ASJ AF: 0.370

Gnomad4 EAS AF: 0.286

Gnomad4 SAS AF: 0.364

Gnomad4 FIN AF: 0.173

Gnomad4 NFE AF: 0.200

Gnomad4 OTH AF: 0.321

Alfa AF: 0.228 Hom.: 8889

Bravo AF: 0.327

Asia WGS AF: 0.380 AC: 1325 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.20
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1369752; hg19: chr10-80248755;