rs8047080

Positions:

• chr16-67368685-A-G

Variant summary

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

The NM_018296.6(LRRC36):​c.1195+1228A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.219 in 152,124 control chromosomes in the GnomAD database, including 7,309 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 0.22 (7309 hom., cov: 32)
• Consequence: LRRC36 NM_018296.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.09

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=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.562 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LRRC36	NM_018296.6	c.1195+1228A>G		intron_variant		ENST00000329956.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LRRC36	ENST00000329956.11	c.1195+1228A>G		intron_variant		1	NM_018296.6	P1

Frequencies

GnomAD3 genomes AF: 0.218 AC: 33155 AN: 152006 Hom.: 7271 Cov.: 32

Gnomad AFR AF: 0.567

Gnomad AMI AF: 0.0780

Gnomad AMR AF: 0.111

Gnomad ASJ AF: 0.0655

Gnomad EAS AF: 0.00462

Gnomad SAS AF: 0.142

Gnomad FIN AF: 0.148

Gnomad MID AF: 0.184

Gnomad NFE AF: 0.0740

Gnomad OTH AF: 0.167

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

GnomAD4 genome AF: 0.219 AC: 33241 AN: 152124 Hom.: 7309 Cov.: 32 AF XY: 0.217 AC XY: 16133 AN XY: 74384

Gnomad4 AFR AF: 0.568

Gnomad4 AMR AF: 0.111

Gnomad4 ASJ AF: 0.0655

Gnomad4 EAS AF: 0.00463

Gnomad4 SAS AF: 0.141

Gnomad4 FIN AF: 0.148

Gnomad4 NFE AF: 0.0740

Gnomad4 OTH AF: 0.166

Alfa AF: 0.123 Hom.: 1487

Bravo AF: 0.228

Asia WGS AF: 0.124 AC: 431 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	5.4
DANN	Benign	0.72

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: rs8047080; hg19: chr16-67402588;