rs718796

Variant names:

• chr7-16579357-T-C
• rs718796
• NM_001195280.2:c.671-717T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001195280.2(LRRC72):​c.671-717T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.081 in 152,224 control chromosomes in the GnomAD database, including 564 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 0.081 (564 hom., cov: 32)
• Consequence: LRRC72 NM_001195280.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0890
• Publications: 3 publications found

Genes affected

LRRC72 (HGNC:42972): (leucine rich repeat containing 72)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.123 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LRRC72	NM_001195280.2	c.671-717T>C		intron_variant	Intron 7 of 8	ENST00000401542.3	NP_001182209.1
LRRC72	XM_011515057.2	c.764-717T>C		intron_variant	Intron 8 of 9		XP_011513359.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LRRC72	ENST00000401542.3	c.671-717T>C		intron_variant	Intron 7 of 8	5	NM_001195280.2	ENSP00000384971.2

Frequencies

GnomAD3 genomes AF: 0.0809 AC: 12306 AN: 152106 Hom.: 563 Cov.: 32

Gnomad AFR AF: 0.126

Gnomad AMI AF: 0.107

Gnomad AMR AF: 0.0669

Gnomad ASJ AF: 0.0654

Gnomad EAS AF: 0.110

Gnomad SAS AF: 0.0207

Gnomad FIN AF: 0.0201

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0686

Gnomad OTH AF: 0.0933

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

GnomAD4 genome AF: 0.0810 AC: 12337 AN: 152224 Hom.: 564 Cov.: 32 AF XY: 0.0764 AC XY: 5685 AN XY: 74422

African (AFR) AF: 0.126 AC: 5230 AN: 41530

American (AMR) AF: 0.0668 AC: 1022 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0654 AC: 227 AN: 3470

East Asian (EAS) AF: 0.110 AC: 568 AN: 5178

South Asian (SAS) AF: 0.0214 AC: 103 AN: 4822

European-Finnish (FIN) AF: 0.0201 AC: 213 AN: 10606

Middle Eastern (MID) AF: 0.0476 AC: 14 AN: 294

European-Non Finnish (NFE) AF: 0.0686 AC: 4665 AN: 68012

Other (OTH) AF: 0.0933 AC: 197 AN: 2112

Alfa AF: 0.0733 Hom.: 624

Bravo AF: 0.0881

Asia WGS AF: 0.0780 AC: 270 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	4.3
DANN	Benign	0.53
PhyloP100		0.089
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: rs718796; hg19: chr7-16618982;