rs17780086

chr17-32016263-G-A

Variant summary

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

The NM_001321350.2(LRRC37B):c.-190-1709G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0983 in 152,164 control chromosomes in the GnomAD database, including 1,007 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 0.098 (1007 hom., cov: 32)
• Consequence: LRRC37B NM_001321350.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.392

Genes affected

LRRC37B (HGNC:29070): (leucine rich repeat containing 37B) Predicted to be integral component of membrane. [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=-0.59).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.141 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LRRC37B	NM_001321350.2	c.-190-1709G>A		intron_variant		ENST00000543378.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LRRC37B	ENST00000543378.7	c.-190-1709G>A		intron_variant		2	NM_001321350.2	A2
LRRC37B	ENST00000579206.5	c.-107-4434G>A		intron_variant		3
LRRC37B	ENST00000583342.1	c.1-5130G>A		intron_variant		2
LRRC37B	ENST00000581370.1	n.98-662G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.0984 AC: 14961 AN: 152046 Hom.: 1008 Cov.: 32

Gnomad AFR AF: 0.0259

Gnomad AMI AF: 0.105

Gnomad AMR AF: 0.0774

Gnomad ASJ AF: 0.173

Gnomad EAS AF: 0.00135

Gnomad SAS AF: 0.149

Gnomad FIN AF: 0.121

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.143

Gnomad OTH AF: 0.103

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

GnomAD4 genome AF: 0.0983 AC: 14955 AN: 152164 Hom.: 1007 Cov.: 32 AF XY: 0.0972 AC XY: 7231 AN XY: 74384

Gnomad4 AFR AF: 0.0258

Gnomad4 AMR AF: 0.0773

Gnomad4 ASJ AF: 0.173

Gnomad4 EAS AF: 0.00135

Gnomad4 SAS AF: 0.149

Gnomad4 FIN AF: 0.121

Gnomad4 NFE AF: 0.143

Gnomad4 OTH AF: 0.101

Alfa AF: 0.129 Hom.: 234

Bravo AF: 0.0896

Asia WGS AF: 0.0620 AC: 215 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.59
Cadd	Benign	9.1
Dann	Benign	0.95

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs17780086; hg19: chr17-30343282;