rs2917666

Variant names:

• chr16-69730057-C-G
• rs2917666
• ENST00000575838.2:n.163+2882C>G

Your query was ambiguous. Multiple possible variants found:

• chr16-69730057-C-G
• chr16-69730057-C-T

Variant summary

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

The NR_186363.1(NQO1-DT):​n.449+2882C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.572 in 151,798 control chromosomes in the GnomAD database, including 26,267 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 0.57 (26267 hom., cov: 31)
• Consequence: NQO1-DT NR_186363.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.51

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=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.677 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NQO1-DT	NR_186363.1	n.449+2882C>G		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NQO1-DT	ENST00000575838.2	n.163+2882C>G		intron_variant	Intron 1 of 1	5
NQO1-DT	ENST00000690354.2	n.566-1362C>G		intron_variant	Intron 1 of 1
NQO1-DT	ENST00000844536.1	n.445+2882C>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.572 AC: 86764 AN: 151680 Hom.: 26261 Cov.: 31

Gnomad AFR AF: 0.419

Gnomad AMI AF: 0.673

Gnomad AMR AF: 0.560

Gnomad ASJ AF: 0.668

Gnomad EAS AF: 0.189

Gnomad SAS AF: 0.483

Gnomad FIN AF: 0.666

Gnomad MID AF: 0.604

Gnomad NFE AF: 0.682

Gnomad OTH AF: 0.577

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

GnomAD4 genome AF: 0.572 AC: 86816 AN: 151798 Hom.: 26267 Cov.: 31 AF XY: 0.565 AC XY: 41882 AN XY: 74156

African (AFR) AF: 0.419 AC: 17336 AN: 41358

American (AMR) AF: 0.560 AC: 8513 AN: 15208

Ashkenazi Jewish (ASJ) AF: 0.668 AC: 2315 AN: 3464

East Asian (EAS) AF: 0.189 AC: 976 AN: 5176

South Asian (SAS) AF: 0.483 AC: 2318 AN: 4804

European-Finnish (FIN) AF: 0.666 AC: 7008 AN: 10530

Middle Eastern (MID) AF: 0.592 AC: 174 AN: 294

European-Non Finnish (NFE) AF: 0.682 AC: 46351 AN: 67952

Other (OTH) AF: 0.577 AC: 1215 AN: 2106

Alfa AF: 0.634 Hom.: 15760

Bravo AF: 0.557

Asia WGS AF: 0.423 AC: 1478 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.75
DANN	Benign	0.50
PhyloP100		-1.5

Splicing

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

Publications

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Other links and lift over

dbSNP: rs2917666; hg19: chr16-69763960;