chr7-150337125-G-T

Variant names:

• chr7-150337125-G-T
• rs200032049
• NM_001142928.2:c.264G>T

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.264G>T​(p.Thr88Thr) 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. Synonymous variant affecting the same amino acid position (i.e. T88T) has been classified as Likely benign.

• Frequency: Genomes: not found (cov: 33)
• Consequence: LRRC61 NM_001142928.2 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.63
• Publications: 1 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=-0.8).
• BP7: Synonymous conserved (PhyloP=-2.63 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.264G>T	p.Thr88Thr	synonymous	Exon 3 of 3	NP_001136400.1	Q9BV99
	LRRC61	NM_001363433.1		c.264G>T	p.Thr88Thr	synonymous	Exon 3 of 3	NP_001350362.1	Q9BV99
	LRRC61	NM_001363434.1		c.264G>T	p.Thr88Thr	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.264G>T	p.Thr88Thr	synonymous	Exon 3 of 3	ENSP00000352642.4	Q9BV99
	LRRC61	ENST00000323078.7	TSL:1	c.264G>T	p.Thr88Thr	synonymous	Exon 2 of 2	ENSP00000339047.6	Q9BV99
	LRRC61	ENST00000493307.1	TSL:5	c.264G>T	p.Thr88Thr	synonymous	Exon 4 of 4	ENSP00000420560.1	Q9BV99

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 36

GnomAD4 genome Cov.: 33

Alfa AF: 0.00 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	0.032
DANN	Benign	0.84
PhyloP100		-2.6

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

Other links and lift over

dbSNP: rs200032049; hg19: chr7-150034214;