chr5-16441477-G-A

Variant names:

• chr5-16441477-G-A
• rs171817
• ENST00000773338.1:n.-234G>A

Variant summary

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

The ENST00000773338.1(ENSG00000300672):​n.-234G>A variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.799 in 152,180 control chromosomes in the GnomAD database, including 48,865 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 0.80 (48865 hom., cov: 33)
• Consequence: ENSG00000300672 ENST00000773338.1 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.03
• Publications: 4 publications found

Genes affected

ENSG00000300672 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.889 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
ENSG00000300672	ENST00000773338.1	n.-234G>A		upstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.799 AC: 121479 AN: 152062 Hom.: 48806 Cov.: 33

Gnomad AFR AF: 0.897

Gnomad AMI AF: 0.778

Gnomad AMR AF: 0.773

Gnomad ASJ AF: 0.767

Gnomad EAS AF: 0.694

Gnomad SAS AF: 0.672

Gnomad FIN AF: 0.793

Gnomad MID AF: 0.737

Gnomad NFE AF: 0.766

Gnomad OTH AF: 0.787

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

GnomAD4 genome AF: 0.799 AC: 121607 AN: 152180 Hom.: 48865 Cov.: 33 AF XY: 0.798 AC XY: 59333 AN XY: 74398

African (AFR) AF: 0.897 AC: 37254 AN: 41526

American (AMR) AF: 0.772 AC: 11806 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.767 AC: 2663 AN: 3472

East Asian (EAS) AF: 0.694 AC: 3583 AN: 5162

South Asian (SAS) AF: 0.673 AC: 3245 AN: 4824

European-Finnish (FIN) AF: 0.793 AC: 8403 AN: 10592

Middle Eastern (MID) AF: 0.748 AC: 220 AN: 294

European-Non Finnish (NFE) AF: 0.766 AC: 52059 AN: 68004

Other (OTH) AF: 0.789 AC: 1668 AN: 2114

Alfa AF: 0.789 Hom.: 8266

Bravo AF: 0.803

Asia WGS AF: 0.737 AC: 2562 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.065
DANN	Benign	0.18
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs171817; hg19: chr5-16441586;