rs4877280

Variant names:

• chr9-84571490-G-A
• rs4877280
• ENST00000650453.1:n.979-11707G>A

Variant summary

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

The ENST00000650453.1(ENSG00000285987):​n.979-11707G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.325 in 152,114 control chromosomes in the GnomAD database, including 8,753 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 0.33 (8753 hom., cov: 33)
• Consequence: ENSG00000285987 ENST00000650453.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.111
• Publications: 8 publications found

Genes affected

ENSG00000285987 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.451 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000650453.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000285987	ENST00000650453.1		n.979-11707G>A		intron	N/A
	ENSG00000285987	ENST00000728338.1		n.1046-11707G>A		intron	N/A
	ENSG00000285987	ENST00000728339.1		n.784-7281G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.325 AC: 49403 AN: 151996 Hom.: 8720 Cov.: 33

Gnomad AFR AF: 0.455

Gnomad AMI AF: 0.315

Gnomad AMR AF: 0.352

Gnomad ASJ AF: 0.270

Gnomad EAS AF: 0.410

Gnomad SAS AF: 0.378

Gnomad FIN AF: 0.264

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.243

Gnomad OTH AF: 0.304

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

GnomAD4 genome AF: 0.325 AC: 49500 AN: 152114 Hom.: 8753 Cov.: 33 AF XY: 0.328 AC XY: 24378 AN XY: 74376

African (AFR) AF: 0.456 AC: 18907 AN: 41464

American (AMR) AF: 0.352 AC: 5384 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.270 AC: 939 AN: 3472

East Asian (EAS) AF: 0.410 AC: 2116 AN: 5162

South Asian (SAS) AF: 0.378 AC: 1823 AN: 4822

European-Finnish (FIN) AF: 0.264 AC: 2800 AN: 10596

Middle Eastern (MID) AF: 0.265 AC: 78 AN: 294

European-Non Finnish (NFE) AF: 0.243 AC: 16511 AN: 67988

Other (OTH) AF: 0.310 AC: 655 AN: 2112

Alfa AF: 0.282 Hom.: 9794

Bravo AF: 0.338

Asia WGS AF: 0.451 AC: 1563 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.44
DANN	Benign	0.43
PhyloP100		0.11

Splicing

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

Other links and lift over

dbSNP: rs4877280; hg19: chr9-87186405;