rs11859352

Positions:

• chr16-67356545-A-G
• chr16-67356545-A-T

Variant summary

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

The NM_018296.6(LRRC36):​c.577+6255A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.254 in 152,114 control chromosomes in the GnomAD database, including 8,999 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 0.25 (8999 hom., cov: 32)
• Consequence: LRRC36 NM_018296.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.715

Genes affected

LRRC36 (HGNC:25615): (leucine rich repeat containing 36)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.616 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LRRC36	NM_018296.6	c.577+6255A>G		intron_variant		ENST00000329956.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LRRC36	ENST00000329956.11	c.577+6255A>G		intron_variant		1	NM_018296.6	P1

Frequencies

GnomAD3 genomes AF: 0.253 AC: 38485 AN: 151996 Hom.: 8960 Cov.: 32

Gnomad AFR AF: 0.622

Gnomad AMI AF: 0.109

Gnomad AMR AF: 0.142

Gnomad ASJ AF: 0.0792

Gnomad EAS AF: 0.0310

Gnomad SAS AF: 0.173

Gnomad FIN AF: 0.157

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.104

Gnomad OTH AF: 0.205

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

GnomAD4 genome AF: 0.254 AC: 38579 AN: 152114 Hom.: 8999 Cov.: 32 AF XY: 0.251 AC XY: 18678 AN XY: 74396

Gnomad4 AFR AF: 0.623

Gnomad4 AMR AF: 0.142

Gnomad4 ASJ AF: 0.0792

Gnomad4 EAS AF: 0.0310

Gnomad4 SAS AF: 0.173

Gnomad4 FIN AF: 0.157

Gnomad4 NFE AF: 0.104

Gnomad4 OTH AF: 0.205

Alfa AF: 0.116 Hom.: 3003

Bravo AF: 0.266

Asia WGS AF: 0.173 AC: 604 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.13
DANN	Benign	0.39

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: rs11859352; hg19: chr16-67390448;