rs7763081

Variant names:

• chr6-53843517-C-A
• rs7763081
• NM_018214.5:c.277+1290C>A

Your query was ambiguous. Multiple possible variants found:

• chr6-53843517-C-A
• chr6-53843517-C-T

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_018214.5(LRRC1):​c.277+1290C>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: 34)
• Consequence: LRRC1 NM_018214.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.124

Genes affected

LRRC1 (HGNC:14307): (leucine rich repeat containing 1) Located in cytosol. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Likely_benign. Variant got -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LRRC1	NM_018214.5	c.277+1290C>A		intron_variant	Intron 2 of 13	ENST00000370888.6	NP_060684.4
LRRC1	XM_017010997.2	c.277+1290C>A		intron_variant	Intron 2 of 10		XP_016866486.1
LRRC1	XR_001743505.2	n.529+1290C>A		intron_variant	Intron 2 of 11
LRRC1	XR_007059279.1	n.529+1290C>A		intron_variant	Intron 2 of 12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LRRC1	ENST00000370888.6	c.277+1290C>A		intron_variant	Intron 2 of 13	1	NM_018214.5	ENSP00000359925.1
LRRC1	ENST00000370882.1	c.277+1290C>A		intron_variant	Intron 2 of 4	3		ENSP00000359919.1
LRRC1	ENST00000487251.5	n.277+1290C>A		intron_variant	Intron 3 of 10	2		ENSP00000435217.1

Frequencies

GnomAD3 genomes Cov.: 34

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

GnomAD4 genome Cov.: 34

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	7.9
DANN	Benign	0.71

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: rs7763081; hg19: chr6-53708315;