rs13194491

Variant names:

• chr6-27069301-C-T
• rs13194491
• ENST00000724244.1:n.190G>A

Variant summary

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

The ENST00000724244.1(LARRPM):​n.190G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0465 in 152,282 control chromosomes in the GnomAD database, including 229 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 0.046 (229 hom., cov: 32)
• Consequence: LARRPM ENST00000724244.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.589
• Publications: 28 publications found

Genes affected

LARRPM (HGNC:56664): (LINC00240 antisense RNA regulating promoter methylation)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.072 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LARRPM	ENST00000724244.1	n.190G>A		non_coding_transcript_exon_variant	Exon 1 of 2
LARRPM	ENST00000724236.1	n.42+126G>A		intron_variant	Intron 1 of 2
LARRPM	ENST00000724237.1	n.42+126G>A		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.0465 AC: 7073 AN: 152164 Hom.: 229 Cov.: 32

Gnomad AFR AF: 0.0266

Gnomad AMI AF: 0.0132

Gnomad AMR AF: 0.0240

Gnomad ASJ AF: 0.0138

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.00165

Gnomad FIN AF: 0.0422

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0737

Gnomad OTH AF: 0.0349

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

GnomAD4 genome AF: 0.0465 AC: 7075 AN: 152282 Hom.: 229 Cov.: 32 AF XY: 0.0431 AC XY: 3211 AN XY: 74472

African (AFR) AF: 0.0266 AC: 1104 AN: 41552

American (AMR) AF: 0.0239 AC: 366 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0138 AC: 48 AN: 3470

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5176

South Asian (SAS) AF: 0.00166 AC: 8 AN: 4830

European-Finnish (FIN) AF: 0.0422 AC: 448 AN: 10624

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.0737 AC: 5015 AN: 68012

Other (OTH) AF: 0.0345 AC: 73 AN: 2114

Alfa AF: 0.0628 Hom.: 1541

Bravo AF: 0.0456

Asia WGS AF: 0.00722 AC: 25 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.2
DANN	Benign	0.64
PhyloP100		-0.59

Splicing

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

Other links and lift over

dbSNP: rs13194491; hg19: chr6-27037080;