rs6002616

Variant names:

• chr22-42108675-A-G
• rs6002616
• ENST00000396387.2:n.279T>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 24 publications found

Genes affected

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

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
OLA1P1		n.42108675A>G		intragenic_variant
NDUFA6-DT	NR_034118.2	n.668-15372A>G		intron_variant	Intron 3 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
OLA1P1	ENST00000396387.2	n.279T>C		non_coding_transcript_exon_variant	Exon 1 of 1	6
NDUFA6-DT	ENST00000417327.5	n.531-15372A>G		intron_variant	Intron 2 of 3	5
NDUFA6-DT	ENST00000434834.5	n.314-15372A>G		intron_variant	Intron 2 of 4	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

African (AFR) AF: 0.380 AC: 8761 AN: 23026

American (AMR) AF: 0.274 AC: 12103 AN: 44100

Ashkenazi Jewish (ASJ) AF: 0.387 AC: 8820 AN: 22778

East Asian (EAS) AF: 0.151 AC: 5687 AN: 37698

South Asian (SAS) AF: 0.369 AC: 27773 AN: 75334

European-Finnish (FIN) AF: 0.381 AC: 20257 AN: 53232

Middle Eastern (MID) AF: 0.398 AC: 1225 AN: 3076

European-Non Finnish (NFE) AF: 0.275 AC: 176222 AN: 641224

Other (OTH) AF: 0.315 AC: 13598 AN: 43232

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

African (AFR) AF: 0.409 AC: 16954 AN: 41474

American (AMR) AF: 0.322 AC: 4925 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.390 AC: 1353 AN: 3472

East Asian (EAS) AF: 0.149 AC: 773 AN: 5184

South Asian (SAS) AF: 0.381 AC: 1831 AN: 4812

European-Finnish (FIN) AF: 0.386 AC: 4071 AN: 10548

Middle Eastern (MID) AF: 0.503 AC: 147 AN: 292

European-Non Finnish (NFE) AF: 0.329 AC: 22363 AN: 67966

Other (OTH) AF: 0.355 AC: 749 AN: 2110

Alfa AF: 0.334 Hom.: 31816

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
PhyloP100		2.1

Splicing

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

Other links and lift over

dbSNP: rs6002616; hg19: chr22-42504679;