5-16286864-A-G

Variant names:

• chr5-16286864-A-G
• rs831657
• ENST00000780293.1:n.242-44955T>C

Variant summary

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

The ENST00000780293.1(ENSG00000301626):​n.242-44955T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.777 in 152,038 control chromosomes in the GnomAD database, including 46,399 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 0.78 (46399 hom., cov: 31)
• Consequence: ENSG00000301626 ENST00000780293.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.118
• Publications: 1 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=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.822 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.242-44955T>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.777 AC: 118001 AN: 151918 Hom.: 46384 Cov.: 31

Gnomad AFR AF: 0.650

Gnomad AMI AF: 0.601

Gnomad AMR AF: 0.797

Gnomad ASJ AF: 0.793

Gnomad EAS AF: 0.795

Gnomad SAS AF: 0.834

Gnomad FIN AF: 0.889

Gnomad MID AF: 0.829

Gnomad NFE AF: 0.828

Gnomad OTH AF: 0.765

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

GnomAD4 genome AF: 0.777 AC: 118058 AN: 152038 Hom.: 46399 Cov.: 31 AF XY: 0.782 AC XY: 58077 AN XY: 74314

African (AFR) AF: 0.649 AC: 26893 AN: 41424

American (AMR) AF: 0.797 AC: 12178 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.793 AC: 2753 AN: 3472

East Asian (EAS) AF: 0.794 AC: 4080 AN: 5138

South Asian (SAS) AF: 0.835 AC: 4021 AN: 4818

European-Finnish (FIN) AF: 0.889 AC: 9410 AN: 10588

Middle Eastern (MID) AF: 0.830 AC: 244 AN: 294

European-Non Finnish (NFE) AF: 0.828 AC: 56320 AN: 68004

Other (OTH) AF: 0.765 AC: 1612 AN: 2108

Alfa AF: 0.807 Hom.: 111022

Bravo AF: 0.760

Asia WGS AF: 0.774 AC: 2694 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	6.4
DANN	Benign	0.85
PhyloP100		0.12

Splicing

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

Other links and lift over

dbSNP: rs831657; hg19: chr5-16286973;