rs1983440

chr7-150326852-G-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+842G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.256 in 152,076 control chromosomes in the GnomAD database, including 5,160 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 0.26 (5160 hom., cov: 32)
• Consequence: LRRC61 NM_001142928.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.68

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=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.405 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LRRC61	NM_001142928.2	c.-145+842G>C		intron_variant		ENST00000359623.9
LRRC61	NM_001363433.1	c.-145+842G>C		intron_variant
LRRC61	NM_001363434.1	c.-145+842G>C		intron_variant
LRRC61	NM_023942.3	c.-145+3292G>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LRRC61	ENST00000359623.9	c.-145+842G>C		intron_variant		2	NM_001142928.2	P1
	ENST00000343855.6	n.744+842G>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.256 AC: 38861 AN: 151956 Hom.: 5167 Cov.: 32

Gnomad AFR AF: 0.239

Gnomad AMI AF: 0.390

Gnomad AMR AF: 0.186

Gnomad ASJ AF: 0.318

Gnomad EAS AF: 0.420

Gnomad SAS AF: 0.291

Gnomad FIN AF: 0.307

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.254

Gnomad OTH AF: 0.240

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

GnomAD4 genome AF: 0.256 AC: 38871 AN: 152076 Hom.: 5160 Cov.: 32 AF XY: 0.259 AC XY: 19269 AN XY: 74326

Gnomad4 AFR AF: 0.239

Gnomad4 AMR AF: 0.185

Gnomad4 ASJ AF: 0.318

Gnomad4 EAS AF: 0.419

Gnomad4 SAS AF: 0.291

Gnomad4 FIN AF: 0.307

Gnomad4 NFE AF: 0.254

Gnomad4 OTH AF: 0.237

Alfa AF: 0.263 Hom.: 564

Bravo AF: 0.246

Asia WGS AF: 0.339 AC: 1181 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	0.020
Dann	Benign	0.63

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		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: rs1983440; hg19: chr7-150023941;