rs5030881

chr10-68544512-G-Achr10-68544512-G-C

Variant summary

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

The ENST00000422205.1(TMEM14DP):n.322C>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 0.932 in 152,174 control chromosomes in the GnomAD database, including 66,253 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 0.93 (66253 hom., cov: 31)
  • Exomes 𝑓: 0.95 (625318 hom.)
  • Failed GnomAD Quality Control
• Consequence: TMEM14DP ENST00000422205.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0970

Genes affected

TMEM14DP (HGNC:15660): (transmembrane protein 14D, pseudogene) Predicted to be involved in mitochondrial transport. Predicted to be integral component of membrane. Predicted to be active in mitochondrial inner membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.962 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
TMEM14DP	ENST00000422205.1	n.322C>T		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.932 AC: 141784 AN: 152056 Hom.: 66212 Cov.: 31

Gnomad AFR AF: 0.879

Gnomad AMI AF: 0.966

Gnomad AMR AF: 0.914

Gnomad ASJ AF: 0.957

Gnomad EAS AF: 0.985

Gnomad SAS AF: 0.911

Gnomad FIN AF: 0.989

Gnomad MID AF: 0.934

Gnomad NFE AF: 0.957

Gnomad OTH AF: 0.922

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.953 AC: 1311924 AN: 1376982 Hom.: 625318 Cov.: 28 AF XY: 0.952 AC XY: 656095 AN XY: 689400

Gnomad4 AFR exome AF: 0.881

Gnomad4 AMR exome AF: 0.925

Gnomad4 ASJ exome AF: 0.946

Gnomad4 EAS exome AF: 0.987

Gnomad4 SAS exome AF: 0.914

Gnomad4 FIN exome AF: 0.987

Gnomad4 NFE exome AF: 0.957

Gnomad4 OTH exome AF: 0.948

GnomAD4 genome AF: 0.932 AC: 141876 AN: 152174 Hom.: 66253 Cov.: 31 AF XY: 0.933 AC XY: 69397 AN XY: 74412

Gnomad4 AFR AF: 0.879

Gnomad4 AMR AF: 0.914

Gnomad4 ASJ AF: 0.957

Gnomad4 EAS AF: 0.985

Gnomad4 SAS AF: 0.911

Gnomad4 FIN AF: 0.989

Gnomad4 NFE AF: 0.957

Gnomad4 OTH AF: 0.922

Alfa AF: 0.942 Hom.: 9619

Bravo AF: 0.926

Asia WGS AF: 0.922 AC: 3208 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	7.7
Dann	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5030881; hg19: chr10-70304269;