15-70944020-T-A

Variant names:

• chr15-70944020-T-A
• rs2119538
• NM_017691.5:c.773+7198T>A

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_017691.5(LRRC49):​c.773+7198T>A variant causes a intron 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: 31)
• Consequence: LRRC49 NM_017691.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.08
• Publications: 1 publications found

Genes affected

LRRC49 (HGNC:25965): (leucine rich repeat containing 49) Predicted to be involved in outer dynein arm assembly. Predicted to be located in microtubule. Predicted to be active in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_017691.5. 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
	LRRC49	NM_017691.5	MANE Select	c.773+7198T>A		intron	N/A	NP_060161.2	Q8IUZ0-1
	LRRC49	NM_001199017.3		c.788+7198T>A		intron	N/A	NP_001185946.1	Q8IUZ0-2
	LRRC49	NM_001284357.2		c.743+7198T>A		intron	N/A	NP_001271286.1	Q8IUZ0-4

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LRRC49	ENST00000260382.10	TSL:1 MANE Select	c.773+7198T>A		intron	N/A	ENSP00000260382.4	Q8IUZ0-1
	LRRC49	ENST00000560369.5	TSL:2	c.788+7198T>A		intron	N/A	ENSP00000453273.1	Q8IUZ0-2
	LRRC49	ENST00000544974.6	TSL:2	c.743+7198T>A		intron	N/A	ENSP00000439600.2	Q8IUZ0-4

Frequencies

GnomAD3 genomes Cov.: 31

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

GnomAD4 genome Cov.: 31

Alfa AF: 0.00 Hom.: 91843

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.088
DANN	Benign	0.36
PhyloP100		-2.1

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: rs2119538; hg19: chr15-71236359;