ENST00000489989.1:n.209T>C

Variant names:

• chr3-103241195-T-C
• rs10511209
• ENST00000489989.1:n.209T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000489989.1(NDUFA4P2):​n.209T>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 0.0398 in 341,790 control chromosomes in the GnomAD database, including 921 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 0.072 (874 hom., cov: 33)
  • Exomes 𝑓: 0.014 (47 hom.)
• Consequence: NDUFA4P2 ENST00000489989.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.192
• Publications: 0 publications found

Genes affected

NDUFA4P2 (HGNC:31362): (NDUFA4 pseudogene 2)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.7).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.193 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000489989.1. 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
	NDUFA4P2	ENST00000489989.1	TSL:6	n.209T>C		non_coding_transcript_exon	Exon 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0722 AC: 10984 AN: 152082 Hom.: 867 Cov.: 33

Gnomad AFR AF: 0.196

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0558

Gnomad ASJ AF: 0.0173

Gnomad EAS AF: 0.0601

Gnomad SAS AF: 0.0224

Gnomad FIN AF: 0.0248

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.0163

Gnomad OTH AF: 0.0632

GnomAD4 exome AF: 0.0136 AC: 2570 AN: 189590 Hom.: 47 Cov.: 0 AF XY: 0.0124 AC XY: 1376 AN XY: 111344

African (AFR) AF: 0.114 AC: 455 AN: 3984

American (AMR) AF: 0.0285 AC: 436 AN: 15314

Ashkenazi Jewish (ASJ) AF: 0.00616 AC: 36 AN: 5844

East Asian (EAS) AF: 0.0281 AC: 186 AN: 6610

South Asian (SAS) AF: 0.00668 AC: 224 AN: 33546

European-Finnish (FIN) AF: 0.0135 AC: 132 AN: 9804

Middle Eastern (MID) AF: 0.0261 AC: 16 AN: 612

European-Non Finnish (NFE) AF: 0.00904 AC: 949 AN: 104980

Other (OTH) AF: 0.0153 AC: 136 AN: 8896

GnomAD4 genome AF: 0.0725 AC: 11027 AN: 152200 Hom.: 874 Cov.: 33 AF XY: 0.0718 AC XY: 5344 AN XY: 74436

African (AFR) AF: 0.197 AC: 8161 AN: 41490

American (AMR) AF: 0.0557 AC: 852 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0173 AC: 60 AN: 3468

East Asian (EAS) AF: 0.0604 AC: 313 AN: 5182

South Asian (SAS) AF: 0.0220 AC: 106 AN: 4828

European-Finnish (FIN) AF: 0.0248 AC: 263 AN: 10614

Middle Eastern (MID) AF: 0.0816 AC: 24 AN: 294

European-Non Finnish (NFE) AF: 0.0163 AC: 1109 AN: 68008

Other (OTH) AF: 0.0654 AC: 138 AN: 2110

Alfa AF: 0.0486 Hom.: 81

Bravo AF: 0.0811

Asia WGS AF: 0.0920 AC: 319 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
CADD	Benign	9.3
DANN	Benign	0.85
PhyloP100		-0.19

Splicing

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

Other links and lift over

dbSNP: rs10511209; hg19: chr3-102960039;