NM_001105659.2:c.574-1898T>A

Variant names:

• chr1-74157764-A-T
• rs10493529
• NM_001105659.2:c.574-1898T>A

Variant summary

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

The NM_001105659.2(LRRIQ3):​c.574-1898T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.303 in 151,886 control chromosomes in the GnomAD database, including 7,742 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 0.30 (7742 hom., cov: 31)
• Consequence: LRRIQ3 NM_001105659.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.913
• Publications: 5 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.382 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001105659.2. 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
	LRRIQ3	NM_001105659.2	MANE Select	c.574-1898T>A		intron	N/A	NP_001099129.1
	LRRIQ3	NM_001322315.2		c.574-1898T>A		intron	N/A	NP_001309244.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LRRIQ3	ENST00000354431.9	TSL:5 MANE Select	c.574-1898T>A		intron	N/A	ENSP00000346414.4
	LRRIQ3	ENST00000395089.5	TSL:5	c.574-1898T>A		intron	N/A	ENSP00000378524.1
	LRRIQ3	ENST00000370909.6	TSL:5	c.250-1898T>A		intron	N/A	ENSP00000359946.2

Frequencies

GnomAD3 genomes AF: 0.303 AC: 46011 AN: 151768 Hom.: 7738 Cov.: 31

Gnomad AFR AF: 0.165

Gnomad AMI AF: 0.305

Gnomad AMR AF: 0.368

Gnomad ASJ AF: 0.306

Gnomad EAS AF: 0.147

Gnomad SAS AF: 0.232

Gnomad FIN AF: 0.310

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.386

Gnomad OTH AF: 0.355

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

GnomAD4 genome AF: 0.303 AC: 46021 AN: 151886 Hom.: 7742 Cov.: 31 AF XY: 0.299 AC XY: 22211 AN XY: 74272

African (AFR) AF: 0.165 AC: 6853 AN: 41464

American (AMR) AF: 0.368 AC: 5601 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.306 AC: 1062 AN: 3468

East Asian (EAS) AF: 0.147 AC: 759 AN: 5152

South Asian (SAS) AF: 0.234 AC: 1129 AN: 4818

European-Finnish (FIN) AF: 0.310 AC: 3275 AN: 10554

Middle Eastern (MID) AF: 0.449 AC: 132 AN: 294

European-Non Finnish (NFE) AF: 0.386 AC: 26192 AN: 67878

Other (OTH) AF: 0.351 AC: 740 AN: 2110

Alfa AF: 0.350 Hom.: 1250

Bravo AF: 0.304

Asia WGS AF: 0.181 AC: 630 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	4.3
DANN	Benign	0.68
PhyloP100		0.91
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: rs10493529; hg19: chr1-74623448;