rs2917666

chr16-69730057-C-Gchr16-69730057-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000575838.1(NQO1-DT):n.163+2882C>G variant causes a intron, non coding transcript 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 ENST00000575838.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.51

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
NQO1-DT	XR_007065098.1	n.162-1362C>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NQO1-DT	ENST00000575838.1	n.163+2882C>G		intron_variant, non_coding_transcript_variant		5
NQO1-DT	ENST00000690354.1	n.409-1362C>G		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.419

Gnomad4 AMR AF: 0.560

Gnomad4 ASJ AF: 0.668

Gnomad4 EAS AF: 0.189

Gnomad4 SAS AF: 0.483

Gnomad4 FIN AF: 0.666

Gnomad4 NFE AF: 0.682

Gnomad4 OTH AF: 0.577

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2917666; hg19: chr16-69763960;