rs4779984

Variant names:

• chr15-32222725-A-G
• rs4779984
• ENST00000780853.1:n.188-14527T>C

Variant summary

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

The ENST00000780853.1(ENSG00000301688):​n.188-14527T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.132 in 151,264 control chromosomes in the GnomAD database, including 1,767 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 0.13 (1767 hom., cov: 30)
• Consequence: ENSG00000301688 ENST00000780853.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.09
• Publications: 5 publications found

Genes affected

ENSG00000301688 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.278 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000780853.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000301688	ENST00000780853.1		n.188-14527T>C		intron	N/A
	ENSG00000301688	ENST00000780854.1		n.241-14527T>C		intron	N/A
	ENSG00000301688	ENST00000780855.1		n.188-14527T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.132 AC: 19934 AN: 151154 Hom.: 1765 Cov.: 30

Gnomad AFR AF: 0.0763

Gnomad AMI AF: 0.130

Gnomad AMR AF: 0.192

Gnomad ASJ AF: 0.142

Gnomad EAS AF: 0.290

Gnomad SAS AF: 0.244

Gnomad FIN AF: 0.155

Gnomad MID AF: 0.151

Gnomad NFE AF: 0.128

Gnomad OTH AF: 0.126

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

GnomAD4 genome AF: 0.132 AC: 19954 AN: 151264 Hom.: 1767 Cov.: 30 AF XY: 0.138 AC XY: 10187 AN XY: 73832

African (AFR) AF: 0.0766 AC: 3151 AN: 41148

American (AMR) AF: 0.192 AC: 2904 AN: 15158

Ashkenazi Jewish (ASJ) AF: 0.142 AC: 492 AN: 3472

East Asian (EAS) AF: 0.290 AC: 1475 AN: 5084

South Asian (SAS) AF: 0.245 AC: 1175 AN: 4800

European-Finnish (FIN) AF: 0.155 AC: 1624 AN: 10454

Middle Eastern (MID) AF: 0.152 AC: 44 AN: 290

European-Non Finnish (NFE) AF: 0.128 AC: 8702 AN: 67858

Other (OTH) AF: 0.128 AC: 268 AN: 2088

Alfa AF: 0.132 Hom.: 1302

Bravo AF: 0.131

Asia WGS AF: 0.240 AC: 826 AN: 3448

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	6.0
DANN	Benign	0.56
PhyloP100		1.1

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs4779984;

hg19: chr15-32514926;