ENST00000689900.3:n.-164A>T

Variant names:

• chr16-30634323-A-T
• rs7194347
• ENST00000689900.3:n.-164A>T

Variant summary

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

The ENST00000689900.3(ENSG00000288983):​n.-164A>T variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.462 in 151,974 control chromosomes in the GnomAD database, including 18,813 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 0.46 (18813 hom., cov: 32)
• Consequence: ENSG00000288983 ENST00000689900.3 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.18
• Publications: 16 publications found

Genes affected

ENSG00000288983 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.68).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.722 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000288983	ENST00000689900.3	n.-164A>T		upstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.462 AC: 70154 AN: 151856 Hom.: 18791 Cov.: 32

Gnomad AFR AF: 0.730

Gnomad AMI AF: 0.424

Gnomad AMR AF: 0.327

Gnomad ASJ AF: 0.359

Gnomad EAS AF: 0.114

Gnomad SAS AF: 0.698

Gnomad FIN AF: 0.334

Gnomad MID AF: 0.379

Gnomad NFE AF: 0.366

Gnomad OTH AF: 0.417

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

GnomAD4 genome AF: 0.462 AC: 70212 AN: 151974 Hom.: 18813 Cov.: 32 AF XY: 0.460 AC XY: 34195 AN XY: 74262

African (AFR) AF: 0.729 AC: 30246 AN: 41484

American (AMR) AF: 0.327 AC: 4983 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.359 AC: 1246 AN: 3470

East Asian (EAS) AF: 0.114 AC: 588 AN: 5180

South Asian (SAS) AF: 0.698 AC: 3358 AN: 4814

European-Finnish (FIN) AF: 0.334 AC: 3529 AN: 10558

Middle Eastern (MID) AF: 0.380 AC: 111 AN: 292

European-Non Finnish (NFE) AF: 0.366 AC: 24886 AN: 67914

Other (OTH) AF: 0.418 AC: 880 AN: 2106

Alfa AF: 0.278 Hom.: 735

Bravo AF: 0.473

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
CADD	Benign	3.6
DANN	Benign	0.27
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs7194347; hg19: chr16-30645644;