17-49486650-T-C

Variant names:

• chr17-49486650-T-C
• rs1035050
• ENST00000832581.1:n.-164A>G

Variant summary

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

The ENST00000832581.1(ENSG00000308220):​n.-164A>G variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.351 in 152,072 control chromosomes in the GnomAD database, including 11,140 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 0.35 (11140 hom., cov: 32)
• Consequence: ENSG00000308220 ENST00000832581.1 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.544
• Publications: 20 publications found

Genes affected

ENSG00000308220 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.745 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
ENSG00000308220	ENST00000832581.1	n.-164A>G		upstream_gene_variant
ENSG00000308220	ENST00000832582.1	n.-164A>G		upstream_gene_variant
ENSG00000308220	ENST00000832583.1	n.-164A>G		upstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.352 AC: 53415 AN: 151954 Hom.: 11145 Cov.: 32

Gnomad AFR AF: 0.137

Gnomad AMI AF: 0.324

Gnomad AMR AF: 0.446

Gnomad ASJ AF: 0.376

Gnomad EAS AF: 0.765

Gnomad SAS AF: 0.452

Gnomad FIN AF: 0.375

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.416

Gnomad OTH AF: 0.401

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

GnomAD4 genome AF: 0.351 AC: 53426 AN: 152072 Hom.: 11140 Cov.: 32 AF XY: 0.353 AC XY: 26216 AN XY: 74348

African (AFR) AF: 0.137 AC: 5701 AN: 41532

American (AMR) AF: 0.446 AC: 6813 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.376 AC: 1304 AN: 3470

East Asian (EAS) AF: 0.765 AC: 3937 AN: 5146

South Asian (SAS) AF: 0.452 AC: 2174 AN: 4806

European-Finnish (FIN) AF: 0.375 AC: 3972 AN: 10598

Middle Eastern (MID) AF: 0.466 AC: 137 AN: 294

European-Non Finnish (NFE) AF: 0.416 AC: 28254 AN: 67914

Other (OTH) AF: 0.397 AC: 839 AN: 2112

Alfa AF: 0.411 Hom.: 45553

Bravo AF: 0.348

Asia WGS AF: 0.539 AC: 1876 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.2
DANN	Benign	0.84
PhyloP100		-0.54

Splicing

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

Other links and lift over

dbSNP: rs1035050; hg19: chr17-47564012;