5-16270490-C-A

Variant names:

• chr5-16270490-C-A
• rs2582660
• ENST00000780293.1:n.242-28581G>T

Variant summary

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

The ENST00000780293.1(ENSG00000301626):​n.242-28581G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.788 in 152,004 control chromosomes in the GnomAD database, including 47,316 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 0.79 (47316 hom., cov: 32)
• Consequence: ENSG00000301626 ENST00000780293.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.152
• 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=-1.05).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.814 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000780293.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000301626	ENST00000780293.1		n.242-28581G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.788 AC: 119681 AN: 151886 Hom.: 47284 Cov.: 32

Gnomad AFR AF: 0.783

Gnomad AMI AF: 0.756

Gnomad AMR AF: 0.698

Gnomad ASJ AF: 0.723

Gnomad EAS AF: 0.754

Gnomad SAS AF: 0.835

Gnomad FIN AF: 0.856

Gnomad MID AF: 0.823

Gnomad NFE AF: 0.804

Gnomad OTH AF: 0.763

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

GnomAD4 genome AF: 0.788 AC: 119768 AN: 152004 Hom.: 47316 Cov.: 32 AF XY: 0.788 AC XY: 58602 AN XY: 74326

African (AFR) AF: 0.783 AC: 32424 AN: 41430

American (AMR) AF: 0.698 AC: 10650 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.723 AC: 2509 AN: 3468

East Asian (EAS) AF: 0.754 AC: 3884 AN: 5152

South Asian (SAS) AF: 0.836 AC: 4028 AN: 4818

European-Finnish (FIN) AF: 0.856 AC: 9046 AN: 10566

Middle Eastern (MID) AF: 0.827 AC: 243 AN: 294

European-Non Finnish (NFE) AF: 0.804 AC: 54689 AN: 67994

Other (OTH) AF: 0.763 AC: 1607 AN: 2106

Alfa AF: 0.785 Hom.: 7661

Bravo AF: 0.771

Asia WGS AF: 0.755 AC: 2622 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.77
DANN	Benign	0.31
PhyloP100		-0.15

Splicing

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

Other links and lift over

dbSNP: rs2582660; hg19: chr5-16270599;