rs2917667

Positions:

• chr16-69729875-A-G
• chr16-69729875-A-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+2700A>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 0.866 in 152,138 control chromosomes in the GnomAD database, including 57,307 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 0.87 (57307 hom., cov: 32)
• Consequence: NQO1-DT ENST00000575838.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.13

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=-1.02).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.905 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NQO1-DT	XR_007065098.1	n.162-1544A>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+2700A>G		intron_variant, non_coding_transcript_variant		5
NQO1-DT	ENST00000690354.1	n.409-1544A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.866 AC: 131707 AN: 152020 Hom.: 57264 Cov.: 32

Gnomad AFR AF: 0.864

Gnomad AMI AF: 0.880

Gnomad AMR AF: 0.918

Gnomad ASJ AF: 0.848

Gnomad EAS AF: 0.642

Gnomad SAS AF: 0.825

Gnomad FIN AF: 0.855

Gnomad MID AF: 0.861

Gnomad NFE AF: 0.879

Gnomad OTH AF: 0.867

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

GnomAD4 genome AF: 0.866 AC: 131803 AN: 152138 Hom.: 57307 Cov.: 32 AF XY: 0.863 AC XY: 64199 AN XY: 74348

Gnomad4 AFR AF: 0.864

Gnomad4 AMR AF: 0.918

Gnomad4 ASJ AF: 0.848

Gnomad4 EAS AF: 0.642

Gnomad4 SAS AF: 0.825

Gnomad4 FIN AF: 0.855

Gnomad4 NFE AF: 0.879

Gnomad4 OTH AF: 0.866

Alfa AF: 0.876 Hom.: 56532

Bravo AF: 0.872

Asia WGS AF: 0.772 AC: 2687 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.1
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2917667; hg19: chr16-69763778;