rs10952250

chr7-150328877-T-C

Variant summary

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

The NM_001142928.2(LRRC61):c.-145+2867T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.306 in 152,084 control chromosomes in the GnomAD database, including 7,591 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 0.31 (7591 hom., cov: 33)
  • Exomes 𝑓: 0.21 (0 hom.)
• Consequence: LRRC61 NM_001142928.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.990

Genes affected

LRRC61 (HGNC:21704): (leucine rich repeat containing 61) Predicted to be active in cytosol. [provided by Alliance of Genome Resources, Apr 2022]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.72).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.408 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LRRC61	NM_001142928.2	c.-145+2867T>C		intron_variant		ENST00000359623.9
LRRC61	NM_001363433.1	c.-145+2867T>C		intron_variant
LRRC61	NM_001363434.1	c.-145+2867T>C		intron_variant
LRRC61	NM_023942.3	c.-145+5317T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LRRC61	ENST00000359623.9	c.-145+2867T>C		intron_variant		2	NM_001142928.2	P1
LRRC61	ENST00000323078.7	c.-145+5317T>C		intron_variant		1		P1
	ENST00000343855.6	n.987T>C		non_coding_transcript_exon_variant	3/3
LRRC61	ENST00000493307.1	c.-145+2867T>C		intron_variant		5		P1

Frequencies

GnomAD3 genomes AF: 0.306 AC: 46456 AN: 151942 Hom.: 7580 Cov.: 33

Gnomad AFR AF: 0.413

Gnomad AMI AF: 0.389

Gnomad AMR AF: 0.202

Gnomad ASJ AF: 0.319

Gnomad EAS AF: 0.420

Gnomad SAS AF: 0.293

Gnomad FIN AF: 0.308

Gnomad MID AF: 0.277

Gnomad NFE AF: 0.255

Gnomad OTH AF: 0.278

GnomAD4 exome AF: 0.208 AC: 5 AN: 24 Hom.: 0 AF XY: 0.250 AC XY: 4 AN XY: 16

Gnomad4 ASJ exome AF: 0.500

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.188

Gnomad4 OTH exome AF: 0.250

GnomAD4 genome AF: 0.306 AC: 46504 AN: 152060 Hom.: 7591 Cov.: 33 AF XY: 0.307 AC XY: 22846 AN XY: 74314

Gnomad4 AFR AF: 0.413

Gnomad4 AMR AF: 0.202

Gnomad4 ASJ AF: 0.319

Gnomad4 EAS AF: 0.419

Gnomad4 SAS AF: 0.292

Gnomad4 FIN AF: 0.308

Gnomad4 NFE AF: 0.255

Gnomad4 OTH AF: 0.275

Alfa AF: 0.265 Hom.: 9289

Bravo AF: 0.303

Asia WGS AF: 0.354 AC: 1234 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
Cadd	Benign	1.4
Dann	Benign	0.64
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.2

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: rs10952250; hg19: chr7-150025966;