rs10511209

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
COXFA4P2		n.103241195T>C		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NDUFA4P2	ENST00000489989.1	n.209T>C		non_coding_transcript_exon_variant	Exon 1 of 1	6

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 v4.3

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;