11-18438761-C-T

Variant names:

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

Variant summary

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

The NM_017448.5(LDHC):​c.710+116C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.891 in 530,570 control chromosomes in the GnomAD database, including 210,738 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 0.90 (61065 hom., cov: 32)
  • Exomes 𝑓: 0.89 (149673 hom.)
• 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: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.932 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LDHC	NM_017448.5	c.710+116C>T		intron_variant	Intron 6 of 7	ENST00000541669.6	NP_059144.1
LDHC	NM_002301.5	c.710+116C>T		intron_variant	Intron 6 of 7		NP_002292.1
LDHC	XM_047426934.1	c.362+116C>T		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>T		intron_variant	Intron 6 of 7	1	NM_017448.5	ENSP00000437783.1

Frequencies

GnomAD3 genomes AF: 0.895 AC: 136170 AN: 152122 Hom.: 61005 Cov.: 32

Gnomad AFR AF: 0.927

Gnomad AMI AF: 0.877

Gnomad AMR AF: 0.851

Gnomad ASJ AF: 0.838

Gnomad EAS AF: 0.953

Gnomad SAS AF: 0.888

Gnomad FIN AF: 0.914

Gnomad MID AF: 0.877

Gnomad NFE AF: 0.882

Gnomad OTH AF: 0.888

GnomAD4 exome AF: 0.889 AC: 336236 AN: 378330 Hom.: 149673 AF XY: 0.888 AC XY: 177133 AN XY: 199544

African (AFR) AF: 0.926 AC: 10167 AN: 10974

American (AMR) AF: 0.857 AC: 13626 AN: 15904

Ashkenazi Jewish (ASJ) AF: 0.840 AC: 9637 AN: 11466

East Asian (EAS) AF: 0.954 AC: 26810 AN: 28106

South Asian (SAS) AF: 0.884 AC: 27989 AN: 31670

European-Finnish (FIN) AF: 0.909 AC: 28300 AN: 31140

Middle Eastern (MID) AF: 0.882 AC: 1920 AN: 2178

European-Non Finnish (NFE) AF: 0.881 AC: 198779 AN: 225560

Other (OTH) AF: 0.891 AC: 19008 AN: 21332

GnomAD4 genome AF: 0.895 AC: 136288 AN: 152240 Hom.: 61065 Cov.: 32 AF XY: 0.896 AC XY: 66687 AN XY: 74414

African (AFR) AF: 0.927 AC: 38517 AN: 41546

American (AMR) AF: 0.851 AC: 13006 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.838 AC: 2911 AN: 3472

East Asian (EAS) AF: 0.954 AC: 4949 AN: 5188

South Asian (SAS) AF: 0.889 AC: 4287 AN: 4824

European-Finnish (FIN) AF: 0.914 AC: 9696 AN: 10604

Middle Eastern (MID) AF: 0.884 AC: 260 AN: 294

European-Non Finnish (NFE) AF: 0.882 AC: 59991 AN: 68006

Other (OTH) AF: 0.885 AC: 1871 AN: 2114

Alfa AF: 0.872 Hom.: 2767

Bravo AF: 0.893

Asia WGS AF: 0.887 AC: 3086 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.8
DANN	Benign	0.55
PhyloP100		-0.19
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: rs2643856; hg19: chr11-18460308;