1-74066303-A-G

Variant names:

• chr1-74066303-A-G
• rs1032082
• NM_001105659.2:c.997+8358T>C

Variant summary

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

The NM_001105659.2(LRRIQ3):​c.997+8358T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.526 in 151,870 control chromosomes in the GnomAD database, including 21,393 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 0.53 (21393 hom., cov: 32)
• Consequence: LRRIQ3 NM_001105659.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.230
• Publications: 3 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=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.798 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.997+8358T>C		intron	N/A	NP_001099129.1
	LRRIQ3	NM_001322315.2		c.997+8358T>C		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.997+8358T>C		intron	N/A	ENSP00000346414.4
	LRRIQ3	ENST00000395089.5	TSL:5	c.997+8358T>C		intron	N/A	ENSP00000378524.1
	LRRIQ3	ENST00000417067.5	TSL:2	c.130+8358T>C		intron	N/A	ENSP00000390376.1

Frequencies

GnomAD3 genomes AF: 0.526 AC: 79798 AN: 151762 Hom.: 21372 Cov.: 32

Gnomad AFR AF: 0.454

Gnomad AMI AF: 0.654

Gnomad AMR AF: 0.509

Gnomad ASJ AF: 0.639

Gnomad EAS AF: 0.819

Gnomad SAS AF: 0.664

Gnomad FIN AF: 0.541

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.532

Gnomad OTH AF: 0.502

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

GnomAD4 genome AF: 0.526 AC: 79858 AN: 151870 Hom.: 21393 Cov.: 32 AF XY: 0.529 AC XY: 39278 AN XY: 74240

African (AFR) AF: 0.454 AC: 18790 AN: 41414

American (AMR) AF: 0.510 AC: 7761 AN: 15228

Ashkenazi Jewish (ASJ) AF: 0.639 AC: 2216 AN: 3470

East Asian (EAS) AF: 0.819 AC: 4231 AN: 5168

South Asian (SAS) AF: 0.663 AC: 3195 AN: 4816

European-Finnish (FIN) AF: 0.541 AC: 5696 AN: 10524

Middle Eastern (MID) AF: 0.473 AC: 139 AN: 294

European-Non Finnish (NFE) AF: 0.532 AC: 36168 AN: 67938

Other (OTH) AF: 0.506 AC: 1066 AN: 2106

Alfa AF: 0.510 Hom.: 4802

Bravo AF: 0.520

Asia WGS AF: 0.695 AC: 2414 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.93
DANN	Benign	0.51
PhyloP100		0.23
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: rs1032082; hg19: chr1-74531987;