rs11859352

Variant names:

• chr16-67356545-A-G
• rs11859352
• NM_018296.6:c.577+6255A>G

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 18 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LRRC36	NM_018296.6	c.577+6255A>G		intron_variant	Intron 5 of 13	ENST00000329956.11	NP_060766.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LRRC36	ENST00000329956.11	c.577+6255A>G		intron_variant	Intron 5 of 13	1	NM_018296.6	ENSP00000329943.6

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

African (AFR) AF: 0.623 AC: 25811 AN: 41444

American (AMR) AF: 0.142 AC: 2174 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.0792 AC: 275 AN: 3472

East Asian (EAS) AF: 0.0310 AC: 161 AN: 5186

South Asian (SAS) AF: 0.173 AC: 832 AN: 4816

European-Finnish (FIN) AF: 0.157 AC: 1660 AN: 10600

Middle Eastern (MID) AF: 0.211 AC: 62 AN: 294

European-Non Finnish (NFE) AF: 0.104 AC: 7073 AN: 68016

Other (OTH) AF: 0.205 AC: 432 AN: 2110

Alfa AF: 0.142 Hom.: 12500

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
PhyloP100		-0.71
Mutation Taster		=100/0	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: rs11859352; hg19: chr16-67390448;