rs4389663

Variant names:

• chr5-105087983-A-T
• rs4389663
• ENST00000503650.1:n.211-201008T>A

Variant summary

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

The ENST00000503650.1(ENSG00000251574):​n.211-201008T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.756 in 152,132 control chromosomes in the GnomAD database, including 44,510 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 0.76 (44510 hom., cov: 33)
• Consequence: ENSG00000251574 ENST00000503650.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0370
• Publications: 3 publications found

Genes affected

ENSG00000251574 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.819 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000503650.1. 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
	ENSG00000251574	ENST00000503650.1	TSL:3	n.211-201008T>A		intron	N/A
	ENSG00000251574	ENST00000522464.1	TSL:3	n.69-79072T>A		intron	N/A
	ENSG00000251574	ENST00000718095.1		n.211-79072T>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.756 AC: 114937 AN: 152014 Hom.: 44481 Cov.: 33

Gnomad AFR AF: 0.681

Gnomad AMI AF: 0.914

Gnomad AMR AF: 0.714

Gnomad ASJ AF: 0.793

Gnomad EAS AF: 0.287

Gnomad SAS AF: 0.714

Gnomad FIN AF: 0.890

Gnomad MID AF: 0.756

Gnomad NFE AF: 0.825

Gnomad OTH AF: 0.754

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

GnomAD4 genome AF: 0.756 AC: 115019 AN: 152132 Hom.: 44510 Cov.: 33 AF XY: 0.757 AC XY: 56267 AN XY: 74362

African (AFR) AF: 0.681 AC: 28270 AN: 41492

American (AMR) AF: 0.714 AC: 10907 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.793 AC: 2749 AN: 3468

East Asian (EAS) AF: 0.286 AC: 1476 AN: 5158

South Asian (SAS) AF: 0.714 AC: 3444 AN: 4824

European-Finnish (FIN) AF: 0.890 AC: 9427 AN: 10598

Middle Eastern (MID) AF: 0.759 AC: 223 AN: 294

European-Non Finnish (NFE) AF: 0.825 AC: 56102 AN: 68004

Other (OTH) AF: 0.754 AC: 1589 AN: 2108

Alfa AF: 0.808 Hom.: 6229

Bravo AF: 0.734

Asia WGS AF: 0.570 AC: 1984 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.7
DANN	Benign	0.40
PhyloP100		-0.037

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: rs4389663;

hg19: chr5-104423684;