NM_001142928.2:c.-145+2867T>C

Variant names:

• chr7-150328877-T-C
• rs10952250
• NM_001142928.2:c.-145+2867T>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 19 publications found

Genes affected

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

ENSG00000293476 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001142928.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LRRC61	NM_001142928.2	MANE Select	c.-145+2867T>C		intron	N/A	NP_001136400.1
	LRRC61	NM_001363433.1		c.-145+2867T>C		intron	N/A	NP_001350362.1
	LRRC61	NM_001363434.1		c.-145+2867T>C		intron	N/A	NP_001350363.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LRRC61	ENST00000359623.9	TSL:2 MANE Select	c.-145+2867T>C		intron	N/A	ENSP00000352642.4
	LRRC61	ENST00000323078.7	TSL:1	c.-145+5317T>C		intron	N/A	ENSP00000339047.6
	ENSG00000293476	ENST00000343855.6	TSL:6	n.987T>C		non_coding_transcript_exon	Exon 3 of 3

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AF: 0.500 AC: 1 AN: 2

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 2

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.188 AC: 3 AN: 16

Other (OTH) AF: 0.250 AC: 1 AN: 4

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

African (AFR) AF: 0.413 AC: 17130 AN: 41450

American (AMR) AF: 0.202 AC: 3089 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.319 AC: 1106 AN: 3470

East Asian (EAS) AF: 0.419 AC: 2167 AN: 5166

South Asian (SAS) AF: 0.292 AC: 1411 AN: 4826

European-Finnish (FIN) AF: 0.308 AC: 3257 AN: 10570

Middle Eastern (MID) AF: 0.253 AC: 74 AN: 292

European-Non Finnish (NFE) AF: 0.255 AC: 17336 AN: 67982

Other (OTH) AF: 0.275 AC: 579 AN: 2108

Alfa AF: 0.272 Hom.: 16138

Bravo AF: 0.303

Asia WGS AF: 0.354 AC: 1234 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	1.4
DANN	Benign	0.64
PhyloP100		-0.99
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.2
Mutation Taster		=99/1	polymorphism (auto)

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: rs10952250; hg19: chr7-150025966;