chr16-69727758-T-G

Variant names:

• chr16-69727758-T-G
• rs689455
• ENST00000575838.2:n.163+583T>G

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+583T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.217 in 152,104 control chromosomes in the GnomAD database, including 3,914 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 0.22 (3914 hom., cov: 32)
• Consequence: NQO1-DT ENST00000575838.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.308
• Publications: 10 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=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.432 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NQO1-DT	NR_186363.1		n.449+583T>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NQO1-DT	ENST00000575838.2	TSL:5	n.163+583T>G		intron	N/A
	NQO1-DT	ENST00000690354.2		n.565+583T>G		intron	N/A
	NQO1-DT	ENST00000844536.1		n.445+583T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.217 AC: 33004 AN: 151986 Hom.: 3907 Cov.: 32

Gnomad AFR AF: 0.187

Gnomad AMI AF: 0.204

Gnomad AMR AF: 0.328

Gnomad ASJ AF: 0.178

Gnomad EAS AF: 0.447

Gnomad SAS AF: 0.332

Gnomad FIN AF: 0.190

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.190

Gnomad OTH AF: 0.238

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.217 AC: 33036 AN: 152104 Hom.: 3914 Cov.: 32 AF XY: 0.223 AC XY: 16607 AN XY: 74336

African (AFR) AF: 0.187 AC: 7783 AN: 41528

American (AMR) AF: 0.328 AC: 5019 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.178 AC: 618 AN: 3468

East Asian (EAS) AF: 0.447 AC: 2296 AN: 5136

South Asian (SAS) AF: 0.333 AC: 1606 AN: 4818

European-Finnish (FIN) AF: 0.190 AC: 2007 AN: 10580

Middle Eastern (MID) AF: 0.248 AC: 73 AN: 294

European-Non Finnish (NFE) AF: 0.190 AC: 12947 AN: 67978

Other (OTH) AF: 0.237 AC: 502 AN: 2114

Alfa AF: 0.196 Hom.: 705

Bravo AF: 0.228

Asia WGS AF: 0.329 AC: 1141 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	4.4
DANN	Benign	0.23
PhyloP100		0.31

Splicing

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

Other links and lift over

dbSNP: rs689455; hg19: chr16-69761661;