5-16286654-T-C

Variant names:

• chr5-16286654-T-C
• rs860545
• ENST00000780293.1:n.242-44745A>G

Variant summary

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

The ENST00000780293.1(ENSG00000301626):​n.242-44745A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.807 in 152,134 control chromosomes in the GnomAD database, including 49,686 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 0.81 (49686 hom., cov: 32)
• Consequence: ENSG00000301626 ENST00000780293.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.361
• Publications: 2 publications found

Genes affected

ENSG00000301626 (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 (SAS) allele frequency at 95% confidence interval = 0.819 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
ENSG00000301626	ENST00000780293.1	n.242-44745A>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.807 AC: 122691 AN: 152016 Hom.: 49671 Cov.: 32

Gnomad AFR AF: 0.781

Gnomad AMI AF: 0.626

Gnomad AMR AF: 0.760

Gnomad ASJ AF: 0.782

Gnomad EAS AF: 0.765

Gnomad SAS AF: 0.835

Gnomad FIN AF: 0.897

Gnomad MID AF: 0.835

Gnomad NFE AF: 0.825

Gnomad OTH AF: 0.780

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

GnomAD4 genome AF: 0.807 AC: 122752 AN: 152134 Hom.: 49686 Cov.: 32 AF XY: 0.810 AC XY: 60251 AN XY: 74342

African (AFR) AF: 0.780 AC: 32399 AN: 41516

American (AMR) AF: 0.760 AC: 11617 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.782 AC: 2714 AN: 3470

East Asian (EAS) AF: 0.765 AC: 3939 AN: 5152

South Asian (SAS) AF: 0.834 AC: 4012 AN: 4808

European-Finnish (FIN) AF: 0.897 AC: 9503 AN: 10590

Middle Eastern (MID) AF: 0.837 AC: 246 AN: 294

European-Non Finnish (NFE) AF: 0.825 AC: 56104 AN: 67994

Other (OTH) AF: 0.780 AC: 1648 AN: 2114

Alfa AF: 0.812 Hom.: 78937

Bravo AF: 0.791

Asia WGS AF: 0.767 AC: 2667 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.9
DANN	Benign	0.70
PhyloP100		0.36

Splicing

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

Other links and lift over

dbSNP: rs860545; hg19: chr5-16286763;