chr17-39932164-T-C

Position:

• chr17-39932164-T-C

Variant summary

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

The NM_001195545.2(LRRC3C):​c.-174-3638T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.589 in 151,824 control chromosomes in the GnomAD database, including 26,541 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 0.59 (26541 hom., cov: 30)
• Consequence: LRRC3C NM_001195545.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.101

Genes affected

LRRC3C (HGNC:40034): (leucine rich repeat containing 3C) Predicted to be integral component of membrane. Predicted to be active in extracellular matrix and extracellular space. [provided by Alliance of Genome Resources, Apr 2022]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.702 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LRRC3C	NM_001195545.2	c.-174-3638T>C		intron_variant		ENST00000377924.6	NP_001182474.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LRRC3C	ENST00000377924.6	c.-174-3638T>C		intron_variant		3	NM_001195545.2	ENSP00000367157	P1
	ENST00000582263.1	n.162-2447T>C		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.589 AC: 89351 AN: 151706 Hom.: 26530 Cov.: 30

Gnomad AFR AF: 0.637

Gnomad AMI AF: 0.416

Gnomad AMR AF: 0.604

Gnomad ASJ AF: 0.601

Gnomad EAS AF: 0.721

Gnomad SAS AF: 0.594

Gnomad FIN AF: 0.491

Gnomad MID AF: 0.649

Gnomad NFE AF: 0.562

Gnomad OTH AF: 0.601

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

GnomAD4 genome AF: 0.589 AC: 89402 AN: 151824 Hom.: 26541 Cov.: 30 AF XY: 0.586 AC XY: 43428 AN XY: 74166

Gnomad4 AFR AF: 0.636

Gnomad4 AMR AF: 0.603

Gnomad4 ASJ AF: 0.601

Gnomad4 EAS AF: 0.721

Gnomad4 SAS AF: 0.594

Gnomad4 FIN AF: 0.491

Gnomad4 NFE AF: 0.562

Gnomad4 OTH AF: 0.601

Alfa AF: 0.571 Hom.: 32510

Bravo AF: 0.606

Asia WGS AF: 0.599 AC: 2085 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	6.6
DANN	Benign	0.61

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs4795405; hg19: chr17-38088417;