NM_018214.5:c.277+1290C>T

Variant names:

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

Variant summary

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

The NM_018214.5(LRRC1):​c.277+1290C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.829 in 152,242 control chromosomes in the GnomAD database, including 52,582 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 0.83 (52582 hom., 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 Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.942 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LRRC1	NM_018214.5	c.277+1290C>T		intron_variant	Intron 2 of 13	ENST00000370888.6	NP_060684.4
LRRC1	XM_017010997.2	c.277+1290C>T		intron_variant	Intron 2 of 10		XP_016866486.1
LRRC1	XR_001743505.2	n.529+1290C>T		intron_variant	Intron 2 of 11
LRRC1	XR_007059279.1	n.529+1290C>T		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>T		intron_variant	Intron 2 of 13	1	NM_018214.5	ENSP00000359925.1
LRRC1	ENST00000370882.1	c.277+1290C>T		intron_variant	Intron 2 of 4	3		ENSP00000359919.1
LRRC1	ENST00000487251.5	n.277+1290C>T		intron_variant	Intron 3 of 10	2		ENSP00000435217.1

Frequencies

GnomAD3 genomes AF: 0.829 AC: 126170 AN: 152124 Hom.: 52538 Cov.: 34

Gnomad AFR AF: 0.764

Gnomad AMI AF: 0.842

Gnomad AMR AF: 0.879

Gnomad ASJ AF: 0.797

Gnomad EAS AF: 0.964

Gnomad SAS AF: 0.861

Gnomad FIN AF: 0.796

Gnomad MID AF: 0.886

Gnomad NFE AF: 0.851

Gnomad OTH AF: 0.855

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

GnomAD4 genome AF: 0.829 AC: 126269 AN: 152242 Hom.: 52582 Cov.: 34 AF XY: 0.829 AC XY: 61682 AN XY: 74446

Gnomad4 AFR AF: 0.764

Gnomad4 AMR AF: 0.879

Gnomad4 ASJ AF: 0.797

Gnomad4 EAS AF: 0.964

Gnomad4 SAS AF: 0.861

Gnomad4 FIN AF: 0.796

Gnomad4 NFE AF: 0.851

Gnomad4 OTH AF: 0.855

Alfa AF: 0.827 Hom.: 6462

Bravo AF: 0.837

Asia WGS AF: 0.876 AC: 3046 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	8.2
DANN	Benign	0.70

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;