rs1709920

chr3-106897997-G-Achr3-106897997-G-Cchr3-106897997-G-T

Variant summary

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

The ENST00000507369.1(MTATP6P22):n.272C>T 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 0.815 in 152,124 control chromosomes in the GnomAD database, including 50,808 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 0.82 (50805 hom., cov: 31)
  • Exomes 𝑓: 0.75 (3 hom.)
• Consequence: MTATP6P22 ENST00000507369.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.899

Genes affected

MTATP6P22 (HGNC:52178): (MT-ATP6 pseudogene 22)

LINC00882 (HGNC:48568): (long intergenic non-protein coding RNA 882)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.68).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.903 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MTATP6P22	ENST00000507369.1	n.272C>T		non_coding_transcript_exon_variant	1/1
LINC00882	ENST00000660862.1	n.659+22969C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.816 AC: 123955 AN: 151998 Hom.: 50805 Cov.: 31

Gnomad AFR AF: 0.742

Gnomad AMI AF: 0.792

Gnomad AMR AF: 0.783

Gnomad ASJ AF: 0.882

Gnomad EAS AF: 0.850

Gnomad SAS AF: 0.925

Gnomad FIN AF: 0.915

Gnomad MID AF: 0.845

Gnomad NFE AF: 0.838

Gnomad OTH AF: 0.817

GnomAD4 exome AF: 0.750 AC: 6 AN: 8 Hom.: 3 Cov.: 0 AF XY: 1.00 AC XY: 2 AN XY: 2

Gnomad4 EAS exome AF: 1.00

Gnomad4 FIN exome AF: 1.00

Gnomad4 NFE exome AF: 0.00

GnomAD4 genome AF: 0.815 AC: 123989 AN: 152116 Hom.: 50805 Cov.: 31 AF XY: 0.819 AC XY: 60860 AN XY: 74354

Gnomad4 AFR AF: 0.741

Gnomad4 AMR AF: 0.782

Gnomad4 ASJ AF: 0.882

Gnomad4 EAS AF: 0.849

Gnomad4 SAS AF: 0.926

Gnomad4 FIN AF: 0.915

Gnomad4 NFE AF: 0.838

Gnomad4 OTH AF: 0.819

Alfa AF: 0.832 Hom.: 10711

Bravo AF: 0.800

Asia WGS AF: 0.878 AC: 3055 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
Cadd	Benign	0.17
Dann	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1709920; hg19: chr3-106616844;