11-78052743-T-G

Variant names:

• chr11-78052743-T-G
• rs627297
• ENST00000530054.1:c.310+20255A>C

Variant summary

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

The ENST00000530054.1(NDUFC2-KCTD14):​c.310+20255A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.223 in 152,060 control chromosomes in the GnomAD database, including 3,843 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 0.22 (3843 hom., cov: 32)
• Consequence: NDUFC2-KCTD14 ENST00000530054.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.396
• Publications: 11 publications found

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

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.239 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NDUFC2-KCTD14	NM_001203260.2	c.311-13985A>C		intron_variant	Intron 2 of 3		NP_001190189.1
NDUFC2-KCTD14	NM_001203261.2	c.310+20255A>C		intron_variant	Intron 2 of 2		NP_001190190.1
NDUFC2-KCTD14	NM_001203262.2	c.167-13985A>C		intron_variant	Intron 1 of 2		NP_001190191.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NDUFC2-KCTD14	ENST00000530054.1	c.310+20255A>C		intron_variant	Intron 2 of 2	2		ENSP00000432614.1
NDUFC2-KCTD14	ENST00000612612.5	c.311-13985A>C		intron_variant	Intron 2 of 3	2		ENSP00000478766.1
NDUFC2-KCTD14	ENST00000614236.2	c.167-13985A>C		intron_variant	Intron 1 of 2	5		ENSP00000481472.1
NDUFC2-KCTD14	ENST00000528251.1	c.166+26836A>C		intron_variant	Intron 1 of 1	4		ENSP00000435967.1

Frequencies

GnomAD3 genomes AF: 0.223 AC: 33886 AN: 151942 Hom.: 3839 Cov.: 32

Gnomad AFR AF: 0.226

Gnomad AMI AF: 0.126

Gnomad AMR AF: 0.245

Gnomad ASJ AF: 0.291

Gnomad EAS AF: 0.0766

Gnomad SAS AF: 0.195

Gnomad FIN AF: 0.199

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.231

Gnomad OTH AF: 0.222

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

GnomAD4 genome AF: 0.223 AC: 33911 AN: 152060 Hom.: 3843 Cov.: 32 AF XY: 0.222 AC XY: 16469 AN XY: 74334

African (AFR) AF: 0.225 AC: 9343 AN: 41452

American (AMR) AF: 0.245 AC: 3742 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.291 AC: 1011 AN: 3472

East Asian (EAS) AF: 0.0774 AC: 401 AN: 5182

South Asian (SAS) AF: 0.196 AC: 945 AN: 4820

European-Finnish (FIN) AF: 0.199 AC: 2104 AN: 10570

Middle Eastern (MID) AF: 0.262 AC: 77 AN: 294

European-Non Finnish (NFE) AF: 0.231 AC: 15711 AN: 67976

Other (OTH) AF: 0.219 AC: 462 AN: 2112

Alfa AF: 0.206 Hom.: 1847

Bravo AF: 0.225

Asia WGS AF: 0.150 AC: 520 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.21
DANN	Benign	0.56
PhyloP100		-0.40
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: rs627297; hg19: chr11-77763789;