NM_001195280.2:c.671-1253A>T

Variant names:

• chr7-16578821-A-T
• rs538537
• NM_001195280.2:c.671-1253A>T

Variant summary

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

The NM_001195280.2(LRRC72):​c.671-1253A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.25 in 152,088 control chromosomes in the GnomAD database, including 4,964 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 (4964 hom., cov: 32)
• Consequence: LRRC72 NM_001195280.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.133
• Publications: 2 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=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.375 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001195280.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LRRC72	NM_001195280.2	MANE Select	c.671-1253A>T		intron	N/A	NP_001182209.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LRRC72	ENST00000401542.3	TSL:5 MANE Select	c.671-1253A>T		intron	N/A	ENSP00000384971.2

Frequencies

GnomAD3 genomes AF: 0.250 AC: 38055 AN: 151970 Hom.: 4965 Cov.: 32

Gnomad AFR AF: 0.256

Gnomad AMI AF: 0.140

Gnomad AMR AF: 0.216

Gnomad ASJ AF: 0.418

Gnomad EAS AF: 0.200

Gnomad SAS AF: 0.390

Gnomad FIN AF: 0.231

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.243

Gnomad OTH AF: 0.285

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

GnomAD4 genome AF: 0.250 AC: 38053 AN: 152088 Hom.: 4964 Cov.: 32 AF XY: 0.252 AC XY: 18725 AN XY: 74344

African (AFR) AF: 0.256 AC: 10612 AN: 41480

American (AMR) AF: 0.215 AC: 3295 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.418 AC: 1451 AN: 3472

East Asian (EAS) AF: 0.200 AC: 1033 AN: 5158

South Asian (SAS) AF: 0.389 AC: 1872 AN: 4808

European-Finnish (FIN) AF: 0.231 AC: 2445 AN: 10584

Middle Eastern (MID) AF: 0.347 AC: 102 AN: 294

European-Non Finnish (NFE) AF: 0.243 AC: 16516 AN: 67970

Other (OTH) AF: 0.284 AC: 599 AN: 2112

Alfa AF: 0.260 Hom.: 644

Bravo AF: 0.246

Asia WGS AF: 0.280 AC: 972 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.8
DANN	Benign	0.84
PhyloP100		0.13
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: rs538537; hg19: chr7-16618446;