7-150337095-T-G

Variant names:

• chr7-150337095-T-G
• NM_001142928.2:c.234T>G
• LRRC61 p.Ala78Ala

Variant summary

Our verdict is Likely benign. The variant received -3 ACMG points: 2P and 5B. PM2 BP4_Strong BP7

The NM_001142928.2(LRRC61):​c.234T>G​(p.Ala78Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 33)
• Consequence: LRRC61 NM_001142928.2 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -5.03
• Publications: 0 publications found

Genes affected

LRRC61 (HGNC:21704): (leucine rich repeat containing 61) Predicted to be active in cytosol. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Likely_benign. The variant received -3 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BP7: Synonymous conserved (PhyloP=-5.03 with no splicing effect.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001142928.2. 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
	LRRC61	NM_001142928.2	MANE Select	c.234T>G	p.Ala78Ala	synonymous	Exon 3 of 3	NP_001136400.1	Q9BV99
	LRRC61	NM_001363433.1		c.234T>G	p.Ala78Ala	synonymous	Exon 3 of 3	NP_001350362.1	Q9BV99
	LRRC61	NM_001363434.1		c.234T>G	p.Ala78Ala	synonymous	Exon 3 of 3	NP_001350363.1	Q9BV99

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LRRC61	ENST00000359623.9	TSL:2 MANE Select	c.234T>G	p.Ala78Ala	synonymous	Exon 3 of 3	ENSP00000352642.4	Q9BV99
	LRRC61	ENST00000323078.7	TSL:1	c.234T>G	p.Ala78Ala	synonymous	Exon 2 of 2	ENSP00000339047.6	Q9BV99
	LRRC61	ENST00000493307.1	TSL:5	c.234T>G	p.Ala78Ala	synonymous	Exon 4 of 4	ENSP00000420560.1	Q9BV99

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 36

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.028
DANN	Benign	0.47
PhyloP100		-5.0

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

hg19: chr7-150034184;