rs2224003

chr6-94446700-C-T

Variant summary

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

The 6-94446700-C-T variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.166 in 152,026 control chromosomes in the GnomAD database, including 2,703 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 0.17 (2703 hom., cov: 32)
  • Exomes 𝑓: 0.19 (0 hom.)
• Consequence: MTCYBP36 ENST00000404146.1 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.393

Genes affected

MTCYBP36 (HGNC:52304): (MT-CYB pseudogene 36)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.233 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MTCYBP36	ENST00000404146.1			downstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.167 AC: 25302 AN: 151892 Hom.: 2703 Cov.: 32

Gnomad AFR AF: 0.0586

Gnomad AMI AF: 0.360

Gnomad AMR AF: 0.182

Gnomad ASJ AF: 0.236

Gnomad EAS AF: 0.0136

Gnomad SAS AF: 0.0824

Gnomad FIN AF: 0.194

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.236

Gnomad OTH AF: 0.176

GnomAD4 exome AF: 0.188 AC: 3 AN: 16 Hom.: 0 Cov.: 0 AF XY: 0.300 AC XY: 3 AN XY: 10

Gnomad4 NFE exome AF: 0.188

GnomAD4 genome AF: 0.166 AC: 25289 AN: 152010 Hom.: 2703 Cov.: 32 AF XY: 0.163 AC XY: 12085 AN XY: 74288

Gnomad4 AFR AF: 0.0584

Gnomad4 AMR AF: 0.182

Gnomad4 ASJ AF: 0.236

Gnomad4 EAS AF: 0.0136

Gnomad4 SAS AF: 0.0820

Gnomad4 FIN AF: 0.194

Gnomad4 NFE AF: 0.236

Gnomad4 OTH AF: 0.174

Alfa AF: 0.208 Hom.: 1688

Bravo AF: 0.163

Asia WGS AF: 0.0500 AC: 175 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	2.7
Dann	Benign	0.54

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs2224003; hg19: chr6-95156418; COSMIC: COSV68189132;