chr7-16530642-G-A

Position:

• chr7-16530642-G-A

Variant summary

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

The NM_001195280.2(LRRC72):​c.91-1853G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.463 in 151,994 control chromosomes in the GnomAD database, including 16,407 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 0.46 (16406 hom., cov: 32)
  • Exomes 𝑓: 0.75 (1 hom.)
• Consequence: LRRC72 NM_001195280.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.21

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=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.592 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LRRC72	NM_001195280.2	c.91-1853G>A		intron_variant		ENST00000401542.3
LRRC72	XM_011515057.2	c.91-1853G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LRRC72	ENST00000401542.3	c.91-1853G>A		intron_variant		5	NM_001195280.2	P1
LRRC72	ENST00000382124.7	c.91-1853G>A		intron_variant, NMD_transcript_variant		3
LRRC72	ENST00000482711.1	n.154-1853G>A		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.463 AC: 70276 AN: 151870 Hom.: 16395 Cov.: 32

Gnomad AFR AF: 0.434

Gnomad AMI AF: 0.589

Gnomad AMR AF: 0.515

Gnomad ASJ AF: 0.377

Gnomad EAS AF: 0.610

Gnomad SAS AF: 0.396

Gnomad FIN AF: 0.488

Gnomad MID AF: 0.388

Gnomad NFE AF: 0.461

Gnomad OTH AF: 0.467

GnomAD4 exome AF: 0.750 AC: 3 AN: 4 Hom.: 1 AF XY: 0.500 AC XY: 1 AN XY: 2

Gnomad4 OTH exome AF: 0.750

GnomAD4 genome AF: 0.463 AC: 70342 AN: 151990 Hom.: 16406 Cov.: 32 AF XY: 0.465 AC XY: 34516 AN XY: 74274

Gnomad4 AFR AF: 0.434

Gnomad4 AMR AF: 0.516

Gnomad4 ASJ AF: 0.377

Gnomad4 EAS AF: 0.610

Gnomad4 SAS AF: 0.394

Gnomad4 FIN AF: 0.488

Gnomad4 NFE AF: 0.461

Gnomad4 OTH AF: 0.472

Alfa AF: 0.460 Hom.: 4320

Bravo AF: 0.468

Asia WGS AF: 0.545 AC: 1895 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	0.17
DANN	Benign	0.33

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: rs7781903; hg19: chr7-16570267;