5-132527285-T-G

Variant names:

• chr5-132527285-T-G
• rs4143832
• ENST00000638452.2:c.-168-31999T>G

Variant summary

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

The ENST00000638452.2(ENSG00000283782):​c.-168-31999T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.762 in 152,142 control chromosomes in the GnomAD database, including 44,732 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 (44732 hom., cov: 32)
• Consequence: ENSG00000283782 ENST00000638452.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.09
• Publications: 56 publications found

Genes affected

ENSG00000283782 (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 = 0.838 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000638452.2. 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
	ENSG00000283782	ENST00000638452.2	TSL:5	c.-168-31999T>G		intron	N/A	ENSP00000492349.2	A0A1W2PQ90
	ENSG00000283782	ENST00000638568.2	TSL:5	c.-310-29047T>G		intron	N/A	ENSP00000491158.2	A0A1W2PQ90
	ENSG00000283782	ENST00000640655.2	TSL:5	c.-168-31999T>G		intron	N/A	ENSP00000491596.2	A0A1W2PQ90

Frequencies

GnomAD3 genomes AF: 0.762 AC: 115838 AN: 152024 Hom.: 44703 Cov.: 32

Gnomad AFR AF: 0.632

Gnomad AMI AF: 0.887

Gnomad AMR AF: 0.841

Gnomad ASJ AF: 0.764

Gnomad EAS AF: 0.860

Gnomad SAS AF: 0.786

Gnomad FIN AF: 0.767

Gnomad MID AF: 0.826

Gnomad NFE AF: 0.810

Gnomad OTH AF: 0.804

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

GnomAD4 genome AF: 0.762 AC: 115922 AN: 152142 Hom.: 44732 Cov.: 32 AF XY: 0.762 AC XY: 56689 AN XY: 74390

African (AFR) AF: 0.632 AC: 26214 AN: 41488

American (AMR) AF: 0.841 AC: 12854 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.764 AC: 2651 AN: 3472

East Asian (EAS) AF: 0.859 AC: 4444 AN: 5172

South Asian (SAS) AF: 0.785 AC: 3789 AN: 4824

European-Finnish (FIN) AF: 0.767 AC: 8121 AN: 10586

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

European-Non Finnish (NFE) AF: 0.810 AC: 55095 AN: 67994

Other (OTH) AF: 0.806 AC: 1701 AN: 2110

Alfa AF: 0.802 Hom.: 221251

Bravo AF: 0.764

Asia WGS AF: 0.815 AC: 2837 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.21
DANN	Benign	0.49
PhyloP100		-2.1

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: rs4143832;

hg19: chr5-131862977;