1-74103068-C-G

Variant names:

• chr1-74103068-C-G
• rs10789388
• NM_001105659.2:c.867+6326G>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.867+6326G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.508 in 151,758 control chromosomes in the GnomAD database, including 20,338 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 0.51 (20338 hom., cov: 31)
• Consequence: LRRIQ3 NM_001105659.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.79
• 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=-0.96).
• 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 rank	MANE	Protein	UniProt
LRRIQ3	NM_001105659.2	c.867+6326G>C		intron_variant	Intron 5 of 7	ENST00000354431.9	NP_001099129.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LRRIQ3	ENST00000354431.9	c.867+6326G>C		intron_variant	Intron 5 of 7	5	NM_001105659.2	ENSP00000346414.4

Frequencies

GnomAD3 genomes AF: 0.508 AC: 77010 AN: 151640 Hom.: 20325 Cov.: 31

Gnomad AFR AF: 0.392

Gnomad AMI AF: 0.654

Gnomad AMR AF: 0.503

Gnomad ASJ AF: 0.638

Gnomad EAS AF: 0.819

Gnomad SAS AF: 0.663

Gnomad FIN AF: 0.541

Gnomad MID AF: 0.465

Gnomad NFE AF: 0.532

Gnomad OTH AF: 0.489

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

GnomAD4 genome AF: 0.508 AC: 77073 AN: 151758 Hom.: 20338 Cov.: 31 AF XY: 0.512 AC XY: 37942 AN XY: 74120

African (AFR) AF: 0.392 AC: 16229 AN: 41408

American (AMR) AF: 0.504 AC: 7655 AN: 15194

Ashkenazi Jewish (ASJ) AF: 0.638 AC: 2212 AN: 3466

East Asian (EAS) AF: 0.819 AC: 4199 AN: 5128

South Asian (SAS) AF: 0.661 AC: 3182 AN: 4814

European-Finnish (FIN) AF: 0.541 AC: 5701 AN: 10542

Middle Eastern (MID) AF: 0.469 AC: 138 AN: 294

European-Non Finnish (NFE) AF: 0.532 AC: 36122 AN: 67892

Other (OTH) AF: 0.493 AC: 1039 AN: 2108

Alfa AF: 0.357 Hom.: 912

Bravo AF: 0.500

Asia WGS AF: 0.690 AC: 2401 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.12
DANN	Benign	0.52
PhyloP100		-1.8
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: rs10789388; hg19: chr1-74568752; COSMIC: COSV63045311;