rs6002616

chr22-42108675-A-G

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000396387.2(OLA1P1):n.279T>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 0.299 in 1,095,756 control chromosomes in the GnomAD database, including 51,761 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 0.35 (9642 hom., cov: 32)
  • Exomes 𝑓: 0.29 (42119 hom.)
• Consequence: OLA1P1 ENST00000396387.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.06

Genes affected

OLA1P1 (HGNC:45274): (OLA1 pseudogene 1)

NDUFA6-DT (HGNC:45273): (NDUFA6 divergent transcript)

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.42).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.404 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NDUFA6-DT	NR_034118.2	n.668-15372A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
OLA1P1	ENST00000396387.2	n.279T>C		non_coding_transcript_exon_variant	1/1
NDUFA6-DT	ENST00000439129.5	n.670-15372A>G		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.351 AC: 53282 AN: 151936 Hom.: 9608 Cov.: 32

Gnomad AFR AF: 0.408

Gnomad AMI AF: 0.216

Gnomad AMR AF: 0.322

Gnomad ASJ AF: 0.390

Gnomad EAS AF: 0.150

Gnomad SAS AF: 0.380

Gnomad FIN AF: 0.386

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.329

Gnomad OTH AF: 0.357

GnomAD4 exome AF: 0.291 AC: 274446 AN: 943700 Hom.: 42119 Cov.: 17 AF XY: 0.299 AC XY: 146391 AN XY: 490174

Gnomad4 AFR exome AF: 0.380

Gnomad4 AMR exome AF: 0.274

Gnomad4 ASJ exome AF: 0.387

Gnomad4 EAS exome AF: 0.151

Gnomad4 SAS exome AF: 0.369

Gnomad4 FIN exome AF: 0.381

Gnomad4 NFE exome AF: 0.275

Gnomad4 OTH exome AF: 0.315

GnomAD4 genome AF: 0.351 AC: 53363 AN: 152056 Hom.: 9642 Cov.: 32 AF XY: 0.354 AC XY: 26311 AN XY: 74312

Gnomad4 AFR AF: 0.409

Gnomad4 AMR AF: 0.322

Gnomad4 ASJ AF: 0.390

Gnomad4 EAS AF: 0.149

Gnomad4 SAS AF: 0.381

Gnomad4 FIN AF: 0.386

Gnomad4 NFE AF: 0.329

Gnomad4 OTH AF: 0.355

Alfa AF: 0.335 Hom.: 12886

Bravo AF: 0.345

Asia WGS AF: 0.277 AC: 960 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.42
Cadd	Benign	12
Dann	Benign	0.91

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6002616; hg19: chr22-42504679;