rs3740713

chr11-18429549-A-C

Variant summary

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

The NM_017448.5(LDHC):c.245-188A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.092 in 152,252 control chromosomes in the GnomAD database, including 856 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 0.092 (856 hom., cov: 32)
• Consequence: LDHC NM_017448.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.30

Genes affected

LDHC (HGNC:6544): (lactate dehydrogenase C) Lactate dehydrogenase C catalyzes the conversion of L-lactate and NAD to pyruvate and NADH in the final step of anaerobic glycolysis. LDHC is testis-specific and belongs to the lactate dehydrogenase family. Two transcript variants have been detected which differ in the 5' untranslated region. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.64).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.125 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LDHC	NM_017448.5	c.245-188A>C		intron_variant		ENST00000541669.6
LDHC	NM_002301.5	c.245-188A>C		intron_variant
LDHC	XM_047426934.1	c.-104-188A>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LDHC	ENST00000541669.6	c.245-188A>C		intron_variant		1	NM_017448.5	P1

Frequencies

GnomAD3 genomes AF: 0.0921 AC: 14009 AN: 152134 Hom.: 855 Cov.: 32

Gnomad AFR AF: 0.0232

Gnomad AMI AF: 0.0888

Gnomad AMR AF: 0.130

Gnomad ASJ AF: 0.123

Gnomad EAS AF: 0.0653

Gnomad SAS AF: 0.115

Gnomad FIN AF: 0.0709

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.127

Gnomad OTH AF: 0.112

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

GnomAD4 genome AF: 0.0920 AC: 14006 AN: 152252 Hom.: 856 Cov.: 32 AF XY: 0.0906 AC XY: 6742 AN XY: 74448

Gnomad4 AFR AF: 0.0231

Gnomad4 AMR AF: 0.130

Gnomad4 ASJ AF: 0.123

Gnomad4 EAS AF: 0.0647

Gnomad4 SAS AF: 0.115

Gnomad4 FIN AF: 0.0709

Gnomad4 NFE AF: 0.127

Gnomad4 OTH AF: 0.111

Alfa AF: 0.128 Hom.: 1759

Bravo AF: 0.0945

Asia WGS AF: 0.0600 AC: 210 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.64
Cadd	Benign	12
Dann	Benign	0.91

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

Publications

LitVar

Other links and lift over

dbSNP: rs3740713; hg19: chr11-18451096;