chr17-64860286-GC-G

Variant names:

• chr17-64860286-GC-G
• rs193920919
• NM_199340.5:c.3859delG

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2

The NM_199340.5(LRRC37A3):​c.3859delG​(p.Ala1287LeufsTer6) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Uncertain significance (no stars). Variant results in nonsense mediated mRNA decay.

• Frequency: Genomes: not found (cov: 31)
• Consequence: LRRC37A3 NM_199340.5 frameshift
• Clinical Significance: Uncertain significance no assertion criteria provided U:1
• Conservation: PhyloP100: 0.0420
• Publications: 0 publications found

Genes affected

LRRC37A3 (HGNC:32427): (leucine rich repeat containing 37 member A3) Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000265218 (HGNC:):

ACMG classification

Our verdict: Uncertain_significance. The variant received 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_199340.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LRRC37A3	NM_199340.5	MANE Select	c.3859delG	p.Ala1287LeufsTer6	frameshift	Exon 12 of 15	NP_955372.2
	LRRC37A3	NM_001303255.3		c.1213delG	p.Ala405LeufsTer6	frameshift	Exon 8 of 11	NP_001290184.1	J3QTJ5

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LRRC37A3	ENST00000584306.6	TSL:1 MANE Select	c.3859delG	p.Ala1287LeufsTer6	frameshift	Exon 12 of 15	ENSP00000464535.1	O60309
	LRRC37A3	ENST00000319651.9	TSL:1	c.3859delG	p.Ala1287LeufsTer6	frameshift	Exon 9 of 12	ENSP00000325713.5	O60309
	LRRC37A3	ENST00000334962.9	TSL:1	c.790delG	p.Ala264LeufsTer6	frameshift	Exon 2 of 5	ENSP00000335617.5	F8W7X0

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome Cov.: 33

GnomAD4 genome Cov.: 31

ClinVar

ClinVar submissions

Significance: Uncertain significance

Revision: no assertion criteria provided

Pathogenic	VUS	Benign	Condition
-	1	-	Prostate cancer (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.042

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs193920919;

hg19: chr17-62856404;

COSMIC: COSV58536290;

COSMIC: COSV58536290;