ENST00000809003.1:n.192+9182G>A

Variant names:

• chr17-46257341-G-A
• rs2458179
• ENST00000809003.1:n.192+9182G>A

Variant summary

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

The ENST00000809003.1(ENSG00000305133):​n.192+9182G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.125 in 150,026 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 0.13 (0 hom., cov: 33)
• Consequence: ENSG00000305133 ENST00000809003.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.709
• Publications: 2 publications found

Genes affected

ENSG00000305133 (HGNC:):

LRRC37A (HGNC:29069): (leucine rich repeat containing 37A) Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.185 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LRRC37A	XM_047437205.1	c.101+9182G>A		intron_variant	Intron 1 of 13		XP_047293161.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000305133	ENST00000809003.1	n.192+9182G>A		intron_variant	Intron 3 of 7

Frequencies

GnomAD3 genomes AF: 0.125 AC: 18798 AN: 149916 Hom.: 0 Cov.: 33

Gnomad AFR AF: 0.0396

Gnomad AMI AF: 0.260

Gnomad AMR AF: 0.157

Gnomad ASJ AF: 0.202

Gnomad EAS AF: 0.00156

Gnomad SAS AF: 0.0628

Gnomad FIN AF: 0.0608

Gnomad MID AF: 0.184

Gnomad NFE AF: 0.188

Gnomad OTH AF: 0.163

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

GnomAD4 genome AF: 0.125 AC: 18787 AN: 150026 Hom.: 0 Cov.: 33 AF XY: 0.118 AC XY: 8631 AN XY: 73354

African (AFR) AF: 0.0395 AC: 1621 AN: 41076

American (AMR) AF: 0.156 AC: 2352 AN: 15050

Ashkenazi Jewish (ASJ) AF: 0.202 AC: 683 AN: 3382

East Asian (EAS) AF: 0.00156 AC: 8 AN: 5120

South Asian (SAS) AF: 0.0629 AC: 297 AN: 4720

European-Finnish (FIN) AF: 0.0608 AC: 637 AN: 10480

Middle Eastern (MID) AF: 0.177 AC: 50 AN: 282

European-Non Finnish (NFE) AF: 0.188 AC: 12573 AN: 66952

Other (OTH) AF: 0.162 AC: 335 AN: 2074

Alfa AF: 0.0491 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	4.3
DANN	Benign	0.94
PhyloP100		-0.71

Splicing

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

Other links and lift over

dbSNP: rs2458179; hg19: chr17-44334707;