rs4795404

Variant names:

• chr17-39929538-A-C
• rs4795404
• NM_001195545.2:c.-175+1724A>C

Your query was ambiguous. Multiple possible variants found:

• chr17-39929538-A-C
• chr17-39929538-A-G
• chr17-39929538-A-T

Variant summary

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

The NM_001195545.2(LRRC3C):​c.-175+1724A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.757 in 152,090 control chromosomes in the GnomAD database, including 43,691 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 0.76 (43683 hom., cov: 32)
  • Exomes 𝑓: 0.94 (8 hom.)
• Consequence: LRRC3C NM_001195545.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0950
• Publications: 14 publications found

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]

ENSG00000264968 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.792 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LRRC3C	NM_001195545.2	c.-175+1724A>C		intron_variant	Intron 1 of 3	ENST00000377924.6	NP_001182474.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LRRC3C	ENST00000377924.6	c.-175+1724A>C		intron_variant	Intron 1 of 3	3	NM_001195545.2	ENSP00000367157.4

Frequencies

GnomAD3 genomes AF: 0.757 AC: 114993 AN: 151954 Hom.: 43673 Cov.: 32

Gnomad AFR AF: 0.703

Gnomad AMI AF: 0.670

Gnomad AMR AF: 0.724

Gnomad ASJ AF: 0.767

Gnomad EAS AF: 0.736

Gnomad SAS AF: 0.774

Gnomad FIN AF: 0.758

Gnomad MID AF: 0.813

Gnomad NFE AF: 0.797

Gnomad OTH AF: 0.763

GnomAD4 exome AF: 0.944 AC: 17 AN: 18 Hom.: 8 AF XY: 1.00 AC XY: 6 AN XY: 6

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 1.00 AC: 6 AN: 6

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.900 AC: 9 AN: 10

Other (OTH) AF: 1.00 AC: 2 AN: 2

GnomAD4 genome AF: 0.756 AC: 115042 AN: 152072 Hom.: 43683 Cov.: 32 AF XY: 0.752 AC XY: 55907 AN XY: 74342

African (AFR) AF: 0.702 AC: 29094 AN: 41438

American (AMR) AF: 0.723 AC: 11053 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.767 AC: 2660 AN: 3466

East Asian (EAS) AF: 0.736 AC: 3820 AN: 5190

South Asian (SAS) AF: 0.774 AC: 3733 AN: 4824

European-Finnish (FIN) AF: 0.758 AC: 7998 AN: 10556

Middle Eastern (MID) AF: 0.816 AC: 240 AN: 294

European-Non Finnish (NFE) AF: 0.797 AC: 54223 AN: 67998

Other (OTH) AF: 0.762 AC: 1610 AN: 2112

Alfa AF: 0.773 Hom.: 10989

Bravo AF: 0.754

Asia WGS AF: 0.721 AC: 2510 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.87
DANN	Benign	0.58
PhyloP100		-0.095

Splicing

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

Other links and lift over

dbSNP: rs4795404; hg19: chr17-38085791;