1-74044121-C-T

Variant summary

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

The NM_001105659.2(LRRIQ3):c.998-2188G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.477 in 151,952 control chromosomes in the GnomAD database, including 18,708 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 0.48 (18708 hom., cov: 32)
• Consequence: LRRIQ3 NM_001105659.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.978

Genes affected

LRRIQ3 (HGNC:28318): (leucine rich repeats and IQ motif containing 3)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.798 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LRRIQ3	NM_001105659.2	c.998-2188G>A		intron_variant		ENST00000354431.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LRRIQ3	ENST00000354431.9	c.998-2188G>A		intron_variant		5	NM_001105659.2	P2
LRRIQ3	ENST00000395089.5	c.998-2188G>A		intron_variant		5		P2
LRRIQ3	ENST00000417067.5	c.131-17152G>A		intron_variant		2
LRRIQ3	ENST00000415760.5	c.*2461-2188G>A		intron_variant, NMD_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.477 AC: 72452 AN: 151834 Hom.: 18702 Cov.: 32

Gnomad AFR AF: 0.285

Gnomad AMI AF: 0.653

Gnomad AMR AF: 0.491

Gnomad ASJ AF: 0.639

Gnomad EAS AF: 0.819

Gnomad SAS AF: 0.664

Gnomad FIN AF: 0.543

Gnomad MID AF: 0.465

Gnomad NFE AF: 0.532

Gnomad OTH AF: 0.466

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

GnomAD4 genome AF: 0.477 AC: 72480 AN: 151952 Hom.: 18708 Cov.: 32 AF XY: 0.482 AC XY: 35829 AN XY: 74288

Gnomad4 AFR AF: 0.284

Gnomad4 AMR AF: 0.492

Gnomad4 ASJ AF: 0.639

Gnomad4 EAS AF: 0.819

Gnomad4 SAS AF: 0.662

Gnomad4 FIN AF: 0.543

Gnomad4 NFE AF: 0.532

Gnomad4 OTH AF: 0.470

Alfa AF: 0.483 Hom.: 2263

Bravo AF: 0.464

Asia WGS AF: 0.681 AC: 2371 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	0.14
Dann	Benign	0.42

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: rs6676622; hg19: chr1-74509805;