rs2643856

Variant names:

• chr11-18438761-C-A
• rs2643856
• NM_017448.5:c.710+116C>A

Your query was ambiguous. Multiple possible variants found:

• chr11-18438761-C-A
• chr11-18438761-C-G
• chr11-18438761-C-T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_017448.5(LDHC):​c.710+116C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: LDHC NM_017448.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.186
• Publications: 14 publications found

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

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LDHC	NM_017448.5	c.710+116C>A		intron_variant	Intron 6 of 7	ENST00000541669.6	NP_059144.1
LDHC	NM_002301.5	c.710+116C>A		intron_variant	Intron 6 of 7		NP_002292.1
LDHC	XM_047426934.1	c.362+116C>A		intron_variant	Intron 4 of 5		XP_047282890.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LDHC	ENST00000541669.6	c.710+116C>A		intron_variant	Intron 6 of 7	1	NM_017448.5	ENSP00000437783.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0 AN: 378884 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 199828

African (AFR) AF: 0.00 AC: 0 AN: 10984

American (AMR) AF: 0.00 AC: 0 AN: 15926

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 11488

East Asian (EAS) AF: 0.00 AC: 0 AN: 28118

South Asian (SAS) AF: 0.00 AC: 0 AN: 31722

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 31170

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2188

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 225922

Other (OTH) AF: 0.00 AC: 0 AN: 21366

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	3.0
DANN	Benign	0.47
PhyloP100		-0.19

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: rs2643856; hg19: chr11-18460308;