ENST00000575838.1:n.163+98C>T

Variant names:

• chr16-69727273-C-T
• rs689457
• ENST00000575838.2:n.163+98C>T

Variant summary

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

The ENST00000575838.2(NQO1-DT):​n.163+98C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0761 in 152,224 control chromosomes in the GnomAD database, including 635 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 0.076 (634 hom., cov: 32)
  • Exomes 𝑓: 0.13 (1 hom.)
• Consequence: NQO1-DT ENST00000575838.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00700
• Publications: 9 publications found

Genes affected

NQO1-DT (HGNC:55344): (NQO1 divergent transcript)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.104 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000575838.2. 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
	NQO1-DT	NR_186363.1		n.449+98C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NQO1-DT	ENST00000575838.2	TSL:5	n.163+98C>T		intron	N/A
	NQO1-DT	ENST00000690354.2		n.565+98C>T		intron	N/A
	NQO1-DT	ENST00000844536.1		n.445+98C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0762 AC: 11585 AN: 152020 Hom.: 634 Cov.: 32

Gnomad AFR AF: 0.0188

Gnomad AMI AF: 0.0362

Gnomad AMR AF: 0.0702

Gnomad ASJ AF: 0.0908

Gnomad EAS AF: 0.000775

Gnomad SAS AF: 0.0340

Gnomad FIN AF: 0.176

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.106

Gnomad OTH AF: 0.0765

GnomAD4 exome AF: 0.128 AC: 11 AN: 86 Hom.: 1 AF XY: 0.106 AC XY: 7 AN XY: 66

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AF: 0.00 AC: 0 AN: 2

European-Finnish (FIN) AF: 0.250 AC: 1 AN: 4

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.111 AC: 8 AN: 72

Other (OTH) AF: 0.333 AC: 2 AN: 6

GnomAD4 genome AF: 0.0761 AC: 11579 AN: 152138 Hom.: 634 Cov.: 32 AF XY: 0.0782 AC XY: 5818 AN XY: 74360

African (AFR) AF: 0.0187 AC: 778 AN: 41532

American (AMR) AF: 0.0701 AC: 1071 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0908 AC: 315 AN: 3470

East Asian (EAS) AF: 0.000777 AC: 4 AN: 5148

South Asian (SAS) AF: 0.0344 AC: 166 AN: 4824

European-Finnish (FIN) AF: 0.176 AC: 1859 AN: 10582

Middle Eastern (MID) AF: 0.0612 AC: 18 AN: 294

European-Non Finnish (NFE) AF: 0.106 AC: 7176 AN: 67976

Other (OTH) AF: 0.0752 AC: 159 AN: 2114

Alfa AF: 0.0975 Hom.: 578

Bravo AF: 0.0662

Asia WGS AF: 0.0210 AC: 73 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	11
DANN	Benign	0.50
PhyloP100		-0.0070

Splicing

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

Other links and lift over

dbSNP: rs689457; hg19: chr16-69761176;