rs9824150

chr3-163116513-T-A

Variant summary

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

The ENST00000490357.1(ENSG00000241168):n.103+90015T>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 0.177 in 151,958 control chromosomes in the GnomAD database, including 2,897 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 0.18 (2897 hom., cov: 32)
• Consequence: ENST00000490357.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.447

Genes affected

(HGNC:):

LINC01192 (HGNC:37197): (long intergenic non-protein coding RNA 1192)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.302 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
	ENST00000490357.1	n.103+90015T>A		intron_variant, non_coding_transcript_variant		5
LINC01192	ENST00000658280.1	n.1318-6355A>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.177 AC: 26919 AN: 151842 Hom.: 2898 Cov.: 32

Gnomad AFR AF: 0.0569

Gnomad AMI AF: 0.363

Gnomad AMR AF: 0.185

Gnomad ASJ AF: 0.186

Gnomad EAS AF: 0.0664

Gnomad SAS AF: 0.315

Gnomad FIN AF: 0.300

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.226

Gnomad OTH AF: 0.166

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

GnomAD4 genome AF: 0.177 AC: 26921 AN: 151958 Hom.: 2897 Cov.: 32 AF XY: 0.182 AC XY: 13482 AN XY: 74242

Gnomad4 AFR AF: 0.0567

Gnomad4 AMR AF: 0.186

Gnomad4 ASJ AF: 0.186

Gnomad4 EAS AF: 0.0668

Gnomad4 SAS AF: 0.315

Gnomad4 FIN AF: 0.300

Gnomad4 NFE AF: 0.226

Gnomad4 OTH AF: 0.166

Alfa AF: 0.201 Hom.: 431

Bravo AF: 0.161

Asia WGS AF: 0.179 AC: 621 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	0.48
Dann	Benign	0.28

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9824150; hg19: chr3-162834301;