rs7801406

Positions:

• chr7-22748655-A-G

Variant summary

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

The ENST00000444653.1(MTCYBP42):​n.150T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.726 in 152,122 control chromosomes in the GnomAD database, including 42,248 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 0.73 (42235 hom., cov: 32)
  • Exomes 𝑓: 0.71 (13 hom.)
• Consequence: MTCYBP42 ENST00000444653.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.702

Genes affected

MTCYBP42 (HGNC:52310): (MT-CYB pseudogene 42)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.62).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 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
MTCYBP42	ENST00000444653.1	n.150T>C		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.726 AC: 110273 AN: 151944 Hom.: 42165 Cov.: 32

Gnomad AFR AF: 0.930

Gnomad AMI AF: 0.615

Gnomad AMR AF: 0.800

Gnomad ASJ AF: 0.759

Gnomad EAS AF: 0.998

Gnomad SAS AF: 0.840

Gnomad FIN AF: 0.477

Gnomad MID AF: 0.826

Gnomad NFE AF: 0.593

Gnomad OTH AF: 0.747

GnomAD4 exome AF: 0.707 AC: 41 AN: 58 Hom.: 13 Cov.: 0 AF XY: 0.750 AC XY: 18 AN XY: 24

Gnomad4 FIN exome AF: 0.704

Gnomad4 NFE exome AF: 0.500

Gnomad4 OTH exome AF: 1.00

GnomAD4 genome AF: 0.726 AC: 110402 AN: 152064 Hom.: 42235 Cov.: 32 AF XY: 0.727 AC XY: 54035 AN XY: 74316

Gnomad4 AFR AF: 0.930

Gnomad4 AMR AF: 0.800

Gnomad4 ASJ AF: 0.759

Gnomad4 EAS AF: 0.998

Gnomad4 SAS AF: 0.840

Gnomad4 FIN AF: 0.477

Gnomad4 NFE AF: 0.593

Gnomad4 OTH AF: 0.749

Alfa AF: 0.631 Hom.: 14033

Bravo AF: 0.761

Asia WGS AF: 0.916 AC: 3182 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.62
CADD	Benign	1.2
DANN	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7801406; hg19: chr7-22788274;