rs10485022

Variant names:

• chr6-94446736-G-A
• rs10485022
• ENST00000404146.1:n.*4C>T

Your query was ambiguous. Multiple possible variants found:

• chr6-94446736-G-A
• chr6-94446736-G-C
• chr6-94446736-G-T

Variant summary

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

The ENST00000404146.1(MTCYBP36):​n.*4C>T variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.194 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MTCYBP36	ENST00000404146.1	n.*4C>T		downstream_gene_variant		6

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;