rs7801406

Variant names:

• chr7-22748655-A-G
• rs7801406
• ENST00000444653.1:n.150T>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 9 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000444653.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MTCYBP42	ENST00000444653.1	TSL:6	n.150T>C		non_coding_transcript_exon	Exon 1 of 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

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) AF: 0.704 AC: 38 AN: 54

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.500 AC: 1 AN: 2

Other (OTH) AF: 1.00 AC: 2 AN: 2

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

African (AFR) AF: 0.930 AC: 38639 AN: 41536

American (AMR) AF: 0.800 AC: 12221 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.759 AC: 2635 AN: 3472

East Asian (EAS) AF: 0.998 AC: 5173 AN: 5182

South Asian (SAS) AF: 0.840 AC: 4045 AN: 4818

European-Finnish (FIN) AF: 0.477 AC: 5030 AN: 10540

Middle Eastern (MID) AF: 0.827 AC: 243 AN: 294

European-Non Finnish (NFE) AF: 0.593 AC: 40272 AN: 67930

Other (OTH) AF: 0.749 AC: 1584 AN: 2114

Alfa AF: 0.634 Hom.: 15881

Bravo AF: 0.761

Asia WGS AF: 0.916 AC: 3182 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.62
CADD	Benign	1.2
DANN	Benign	0.37
PhyloP100		0.70

Splicing

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

Other links and lift over

dbSNP: rs7801406; hg19: chr7-22788274;