3-169810661-C-T

Variant names:

• chr3-169810661-C-T
• rs10936601
• NM_001172779.2:c.139+1749G>A

Variant summary

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

The NM_001172779.2(LRRC34):​c.139+1749G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.37 in 152,080 control chromosomes in the GnomAD database, including 11,771 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 0.37 (11771 hom., cov: 33)
• Consequence: LRRC34 NM_001172779.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.335
• Publications: 43 publications found

Genes affected

LRRC34 (HGNC:28408): (leucine rich repeat containing 34) Predicted to be involved in cell differentiation. Predicted to be located in cytoplasm and nucleolus. [provided by Alliance of Genome Resources, Apr 2022]

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 = 0.665 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LRRC34	NM_001172779.2	c.139+1749G>A		intron_variant	Intron 1 of 10	ENST00000446859.7	NP_001166250.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LRRC34	ENST00000446859.7	c.139+1749G>A		intron_variant	Intron 1 of 10	2	NM_001172779.2	ENSP00000414635.1

Frequencies

GnomAD3 genomes AF: 0.370 AC: 56183 AN: 151962 Hom.: 11728 Cov.: 33

Gnomad AFR AF: 0.527

Gnomad AMI AF: 0.237

Gnomad AMR AF: 0.408

Gnomad ASJ AF: 0.220

Gnomad EAS AF: 0.684

Gnomad SAS AF: 0.363

Gnomad FIN AF: 0.274

Gnomad MID AF: 0.320

Gnomad NFE AF: 0.267

Gnomad OTH AF: 0.363

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

GnomAD4 genome AF: 0.370 AC: 56279 AN: 152080 Hom.: 11771 Cov.: 33 AF XY: 0.372 AC XY: 27677 AN XY: 74344

African (AFR) AF: 0.528 AC: 21895 AN: 41454

American (AMR) AF: 0.408 AC: 6244 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.220 AC: 764 AN: 3470

East Asian (EAS) AF: 0.684 AC: 3533 AN: 5164

South Asian (SAS) AF: 0.363 AC: 1748 AN: 4822

European-Finnish (FIN) AF: 0.274 AC: 2897 AN: 10574

Middle Eastern (MID) AF: 0.316 AC: 93 AN: 294

European-Non Finnish (NFE) AF: 0.266 AC: 18118 AN: 67996

Other (OTH) AF: 0.366 AC: 771 AN: 2106

Alfa AF: 0.307 Hom.: 22646

Bravo AF: 0.394

Asia WGS AF: 0.523 AC: 1814 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	0.75
DANN	Benign	0.43
PhyloP100		-0.34
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: rs10936601; hg19: chr3-169528449;