rs5030881

Variant names:

• chr10-68544512-G-A
• rs5030881
• ENST00000422205.1:n.322C>T

Your query was ambiguous. Multiple possible variants found:

• chr10-68544512-G-A
• chr10-68544512-G-C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000422205.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TMEM14DP	ENST00000422205.1	TSL:6	n.322C>T		non_coding_transcript_exon	Exon 1 of 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

African (AFR) AF: 0.881 AC: 27876 AN: 31646

American (AMR) AF: 0.925 AC: 41204 AN: 44524

Ashkenazi Jewish (ASJ) AF: 0.946 AC: 24214 AN: 25588

East Asian (EAS) AF: 0.987 AC: 38719 AN: 39244

South Asian (SAS) AF: 0.914 AC: 77169 AN: 84476

European-Finnish (FIN) AF: 0.987 AC: 52527 AN: 53236

Middle Eastern (MID) AF: 0.942 AC: 4485 AN: 4760

European-Non Finnish (NFE) AF: 0.957 AC: 991347 AN: 1036144

Other (OTH) AF: 0.948 AC: 54383 AN: 57364

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

African (AFR) AF: 0.879 AC: 36462 AN: 41494

American (AMR) AF: 0.914 AC: 13932 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.957 AC: 3322 AN: 3470

East Asian (EAS) AF: 0.985 AC: 5108 AN: 5186

South Asian (SAS) AF: 0.911 AC: 4395 AN: 4824

European-Finnish (FIN) AF: 0.989 AC: 10485 AN: 10602

Middle Eastern (MID) AF: 0.922 AC: 271 AN: 294

European-Non Finnish (NFE) AF: 0.957 AC: 65072 AN: 68030

Other (OTH) AF: 0.922 AC: 1948 AN: 2112

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	7.7
DANN	Benign	0.38
PhyloP100		-0.097

Splicing

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

Other links and lift over

dbSNP: rs5030881; hg19: chr10-70304269;