rs9071

Positions:

• chr8-144525122-G-A
• chr8-144525122-G-C

Variant summary

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

The NM_014665.4(LRRC14):​c.*3644G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.486 in 793,018 control chromosomes in the GnomAD database, including 96,068 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 0.54 (22648 hom., cov: 35)
  • Exomes 𝑓: 0.47 (73420 hom.)
• Consequence: LRRC14 NM_014665.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.275

Genes affected

LRRC14 (HGNC:20419): (leucine rich repeat containing 14) This gene encodes a leucine-rich repeat-containing protein. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Dec 2012]

LRRC24 (HGNC:28947): (leucine rich repeat containing 24) Predicted to act upstream of or within positive regulation of synapse assembly. Predicted to be integral component of membrane. Predicted to be active in extracellular matrix and extracellular space. [provided by Alliance of Genome Resources, Apr 2022]

LRRC14 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.643 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LRRC14	NM_014665.4	c.*3644G>A		3_prime_UTR_variant	4/4	ENST00000292524.6	NP_055480.1
LRRC24	NM_001024678.4	c.-59-89C>T		intron_variant		ENST00000529415.7	NP_001019849.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LRRC14	ENST00000292524.6	c.*3644G>A		3_prime_UTR_variant	4/4	1	NM_014665.4	ENSP00000292524.1
LRRC24	ENST00000529415.7	c.-59-89C>T		intron_variant		1	NM_001024678.4	ENSP00000434849.1
LRRC24	ENST00000533758.1	c.-59-89C>T		intron_variant		5		ENSP00000435653.1

Frequencies

GnomAD3 genomes AF: 0.539 AC: 81940 AN: 152100 Hom.: 22614 Cov.: 35

Gnomad AFR AF: 0.649

Gnomad AMI AF: 0.269

Gnomad AMR AF: 0.566

Gnomad ASJ AF: 0.480

Gnomad EAS AF: 0.481

Gnomad SAS AF: 0.587

Gnomad FIN AF: 0.501

Gnomad MID AF: 0.465

Gnomad NFE AF: 0.479

Gnomad OTH AF: 0.535

GnomAD4 exome AF: 0.473 AC: 303029 AN: 640800 Hom.: 73420 Cov.: 9 AF XY: 0.476 AC XY: 150469 AN XY: 316250

Gnomad4 AFR exome AF: 0.637

Gnomad4 AMR exome AF: 0.561

Gnomad4 ASJ exome AF: 0.478

Gnomad4 EAS exome AF: 0.410

Gnomad4 SAS exome AF: 0.572

Gnomad4 FIN exome AF: 0.495

Gnomad4 NFE exome AF: 0.463

Gnomad4 OTH exome AF: 0.487

GnomAD4 genome AF: 0.539 AC: 82024 AN: 152218 Hom.: 22648 Cov.: 35 AF XY: 0.543 AC XY: 40382 AN XY: 74426

Gnomad4 AFR AF: 0.649

Gnomad4 AMR AF: 0.567

Gnomad4 ASJ AF: 0.480

Gnomad4 EAS AF: 0.480

Gnomad4 SAS AF: 0.588

Gnomad4 FIN AF: 0.501

Gnomad4 NFE AF: 0.479

Gnomad4 OTH AF: 0.534

Alfa AF: 0.494 Hom.: 21472

Bravo AF: 0.547

Asia WGS AF: 0.578 AC: 2009 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	3.3
DANN	Benign	0.67

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: rs9071; hg19: chr8-145750506;