rs17660212

Variant names:

• chr16-2868291-A-G
• rs17660212
• ENST00000575693.2:n.-72T>C

Variant summary

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

The ENST00000575693.2(ENSG00000263280):​n.-72T>C variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.265 in 152,214 control chromosomes in the GnomAD database, including 6,925 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 0.26 (6925 hom., cov: 34)
• Consequence: ENSG00000263280 ENST00000575693.2 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.07

Genes affected

ENSG00000263280 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.388 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101929566	NR_188573.1	n.-87T>C		upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000263280	ENST00000575693.2	n.-72T>C		upstream_gene_variant		3
ENSG00000263280	ENST00000659109.1	n.-87T>C		upstream_gene_variant
ENSG00000263280	ENST00000662388.1	n.-40T>C		upstream_gene_variant
ENSG00000263280	ENST00000691941.1	n.-95T>C		upstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.265 AC: 40327 AN: 152096 Hom.: 6927 Cov.: 34

Gnomad AFR AF: 0.0805

Gnomad AMI AF: 0.286

Gnomad AMR AF: 0.274

Gnomad ASJ AF: 0.423

Gnomad EAS AF: 0.00270

Gnomad SAS AF: 0.0988

Gnomad FIN AF: 0.297

Gnomad MID AF: 0.377

Gnomad NFE AF: 0.392

Gnomad OTH AF: 0.337

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

GnomAD4 genome AF: 0.265 AC: 40313 AN: 152214 Hom.: 6925 Cov.: 34 AF XY: 0.256 AC XY: 19014 AN XY: 74390

Gnomad4 AFR AF: 0.0803

Gnomad4 AMR AF: 0.273

Gnomad4 ASJ AF: 0.423

Gnomad4 EAS AF: 0.00270

Gnomad4 SAS AF: 0.0998

Gnomad4 FIN AF: 0.297

Gnomad4 NFE AF: 0.391

Gnomad4 OTH AF: 0.334

Alfa AF: 0.346 Hom.: 4671

Bravo AF: 0.258

Asia WGS AF: 0.0570 AC: 199 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.42
DANN	Benign	0.25

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17660212; hg19: chr16-2918292;