chr9-79548398-C-T

Variant names:

• chr9-79548398-C-T
• rs11138290
• ENST00000656806.2:n.161-16064G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000656806.2(LNCARSR):​n.161-16064G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0636 in 151,920 control chromosomes in the GnomAD database, including 386 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 0.064 (386 hom., cov: 30)
• Consequence: LNCARSR ENST00000656806.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.588
• Publications: 3 publications found

Genes affected

LNCARSR (HGNC:53864): (lncRNA regulator of Akt signaling associated with HCC and RCC)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.131 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LNCARSR	NR_184110.1	n.326-16064G>A		intron_variant	Intron 1 of 3
LNCARSR	NR_184111.1	n.326-16064G>A		intron_variant	Intron 1 of 2
LNCARSR	NR_184112.1	n.322-16064G>A		intron_variant	Intron 1 of 3
LNCARSR	NR_184113.1	n.322-16064G>A		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LNCARSR	ENST00000656806.2	n.161-16064G>A		intron_variant	Intron 1 of 2
LNCARSR	ENST00000665514.1	n.151-16064G>A		intron_variant	Intron 1 of 3
LNCARSR	ENST00000666862.1	n.143-14215G>A		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.0636 AC: 9662 AN: 151802 Hom.: 388 Cov.: 30

Gnomad AFR AF: 0.0851

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0513

Gnomad ASJ AF: 0.0314

Gnomad EAS AF: 0.140

Gnomad SAS AF: 0.0734

Gnomad FIN AF: 0.146

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0367

Gnomad OTH AF: 0.0692

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

GnomAD4 genome AF: 0.0636 AC: 9663 AN: 151920 Hom.: 386 Cov.: 30 AF XY: 0.0696 AC XY: 5164 AN XY: 74214

African (AFR) AF: 0.0850 AC: 3523 AN: 41434

American (AMR) AF: 0.0511 AC: 781 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.0314 AC: 109 AN: 3470

East Asian (EAS) AF: 0.140 AC: 719 AN: 5140

South Asian (SAS) AF: 0.0733 AC: 353 AN: 4818

European-Finnish (FIN) AF: 0.146 AC: 1533 AN: 10516

Middle Eastern (MID) AF: 0.0374 AC: 11 AN: 294

European-Non Finnish (NFE) AF: 0.0367 AC: 2492 AN: 67964

Other (OTH) AF: 0.0676 AC: 142 AN: 2102

Alfa AF: 0.0524 Hom.: 23

Bravo AF: 0.0590

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	6.9
DANN	Benign	0.87
PhyloP100		0.59

Splicing

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

Other links and lift over

dbSNP: rs11138290; hg19: chr9-82163313;