rs627297

Positions:

• chr11-78052743-T-A
• chr11-78052743-T-C
• chr11-78052743-T-G

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001203260.2(NDUFC2-KCTD14):​c.311-13985A>T 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)
• Consequence: NDUFC2-KCTD14 NM_001203260.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.396

Genes affected

NDUFC2-KCTD14 (HGNC:42956): (NDUFC2-KCTD14 readthrough) This locus represents naturally occurring read-through transcription between the neighboring NDUFC2 (NADH dehydrogenase (ubiquinone) 1, subcomplex unknown, 2, 14.5kDa) and KCTD14 (potassium channel tetramerisation domain containing 14) genes on chromosome 11. The read-through transcripts share sequence identity with the upstream gene product and one variant has a frameshifted C-terminal region derived from the downstream gene exons. [provided by RefSeq, Feb 2011]

ACMG classification

Verdict is Likely_benign. Variant got -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NDUFC2-KCTD14	NM_001203260.2	c.311-13985A>T		intron_variant			NP_001190189.1
NDUFC2-KCTD14	NM_001203261.2	c.310+20255A>T		intron_variant			NP_001190190.1
NDUFC2-KCTD14	NM_001203262.2	c.167-13985A>T		intron_variant			NP_001190191.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NDUFC2-KCTD14	ENST00000612612.5	c.311-13985A>T		intron_variant		2		ENSP00000478766.1
NDUFC2-KCTD14	ENST00000530054.1	c.310+20255A>T		intron_variant		2		ENSP00000432614.1
NDUFC2-KCTD14	ENST00000614236.2	c.167-13985A>T		intron_variant		5		ENSP00000481472.1
NDUFC2-KCTD14	ENST00000528251.1	c.166+26836A>T		intron_variant		4		ENSP00000435967.1

Frequencies

GnomAD3 genomes Cov.: 32

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

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.20
DANN	Benign	0.63

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: rs627297; hg19: chr11-77763789;