15-70944020-T-C

Position:

• chr15-70944020-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_017691.5(LRRC49):​c.773+7198T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.962 in 152,248 control chromosomes in the GnomAD database, including 70,550 homozygotes. 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 0.96 (70550 hom., cov: 31)
• Consequence: LRRC49 NM_017691.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.08

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.984 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LRRC49	NM_017691.5	c.773+7198T>C		intron_variant		ENST00000260382.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LRRC49	ENST00000260382.10	c.773+7198T>C		intron_variant		1	NM_017691.5	P4

Frequencies

GnomAD3 genomes AF: 0.962 AC: 146294 AN: 152126 Hom.: 70498 Cov.: 31

Gnomad AFR AF: 0.889

Gnomad AMI AF: 0.995

Gnomad AMR AF: 0.984

Gnomad ASJ AF: 0.972

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.991

Gnomad FIN AF: 0.995

Gnomad MID AF: 0.972

Gnomad NFE AF: 0.990

Gnomad OTH AF: 0.963

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

GnomAD4 genome AF: 0.962 AC: 146408 AN: 152248 Hom.: 70550 Cov.: 31 AF XY: 0.963 AC XY: 71671 AN XY: 74432

Gnomad4 AFR AF: 0.889

Gnomad4 AMR AF: 0.984

Gnomad4 ASJ AF: 0.972

Gnomad4 EAS AF: 1.00

Gnomad4 SAS AF: 0.990

Gnomad4 FIN AF: 0.995

Gnomad4 NFE AF: 0.990

Gnomad4 OTH AF: 0.963

Alfa AF: 0.984 Hom.: 70441

Bravo AF: 0.958

Asia WGS AF: 0.990 AC: 3443 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.10
DANN	Benign	0.52

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

Publications

LitVar

Other links and lift over

dbSNP: rs2119538; hg19: chr15-71236359;