7-16578821-A-T

Position:

• chr7-16578821-A-T

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LRRC72	NM_001195280.2	c.671-1253A>T		intron_variant		ENST00000401542.3	NP_001182209.1
LRRC72	XM_011515057.2	c.764-1253A>T		intron_variant			XP_011513359.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LRRC72	ENST00000401542.3	c.671-1253A>T		intron_variant		5	NM_001195280.2	ENSP00000384971	P1

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

Gnomad4 AFR AF: 0.256

Gnomad4 AMR AF: 0.215

Gnomad4 ASJ AF: 0.418

Gnomad4 EAS AF: 0.200

Gnomad4 SAS AF: 0.389

Gnomad4 FIN AF: 0.231

Gnomad4 NFE AF: 0.243

Gnomad4 OTH AF: 0.284

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.8
DANN	Benign	0.84

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: rs538537; hg19: chr7-16618446;