chr6-94446736-G-A

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.333 AC: 2 AN: 6

Other (OTH) AC: 0 AN: 0

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

African (AFR) AF: 0.107 AC: 4452 AN: 41514

American (AMR) AF: 0.248 AC: 3780 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.251 AC: 868 AN: 3464

East Asian (EAS) AF: 0.121 AC: 623 AN: 5142

South Asian (SAS) AF: 0.153 AC: 738 AN: 4818

European-Finnish (FIN) AF: 0.194 AC: 2053 AN: 10558

Middle Eastern (MID) AF: 0.173 AC: 51 AN: 294

European-Non Finnish (NFE) AF: 0.237 AC: 16127 AN: 67978

Other (OTH) AF: 0.198 AC: 417 AN: 2108

Alfa AF: 0.221 Hom.: 7579

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
PhyloP100		2.8

Splicing

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

Other links and lift over

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