rs10485022

Positions:

• chr6-94446736-G-A

Variant summary

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

The 6-94446736-G-A variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.194 in 152,052 control chromosomes in the GnomAD database, including 3,241 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 0.19 (3240 hom., cov: 32)
  • Exomes 𝑓: 0.33 (1 hom.)
• Consequence: MTCYBP36 ENST00000404146.1 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.76

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=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.241 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.194 AC: 29410 AN: 151928 Hom.: 3231 Cov.: 32

Gnomad AFR AF: 0.107

Gnomad AMI AF: 0.361

Gnomad AMR AF: 0.247

Gnomad ASJ AF: 0.251

Gnomad EAS AF: 0.121

Gnomad SAS AF: 0.153

Gnomad FIN AF: 0.194

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.237

Gnomad OTH AF: 0.196

GnomAD4 exome AF: 0.333 AC: 2 AN: 6 Hom.: 1 Cov.: 0 AF XY: 0.500 AC XY: 2 AN XY: 4

Gnomad4 NFE exome AF: 0.333

GnomAD4 genome AF: 0.194 AC: 29437 AN: 152046 Hom.: 3240 Cov.: 32 AF XY: 0.192 AC XY: 14285 AN XY: 74292

Gnomad4 AFR AF: 0.107

Gnomad4 AMR AF: 0.248

Gnomad4 ASJ AF: 0.251

Gnomad4 EAS AF: 0.121

Gnomad4 SAS AF: 0.153

Gnomad4 FIN AF: 0.194

Gnomad4 NFE AF: 0.237

Gnomad4 OTH AF: 0.198

Alfa AF: 0.218 Hom.: 2193

Bravo AF: 0.196

Asia WGS AF: 0.175 AC: 608 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	6.5
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10485022; hg19: chr6-95156454; COSMIC: COSV68189134;