4-32588426-C-T

Variant names:

• chr4-32588426-C-T
• rs1037079
• ENST00000659320.1:n.216-3130G>A

Variant summary

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

The ENST00000659320.1(ENSG00000286784):​n.216-3130G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.127 in 151,796 control chromosomes in the GnomAD database, including 2,151 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 (2151 hom., cov: 32)
• Consequence: ENSG00000286784 ENST00000659320.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.34
• Publications: 3 publications found

Genes affected

ENSG00000286784 (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 = 0.55 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000286784	ENST00000659320.1	n.216-3130G>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.127 AC: 19214 AN: 151678 Hom.: 2148 Cov.: 32

Gnomad AFR AF: 0.211

Gnomad AMI AF: 0.0307

Gnomad AMR AF: 0.115

Gnomad ASJ AF: 0.0202

Gnomad EAS AF: 0.568

Gnomad SAS AF: 0.228

Gnomad FIN AF: 0.114

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.0469

Gnomad OTH AF: 0.114

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

GnomAD4 genome AF: 0.127 AC: 19248 AN: 151796 Hom.: 2151 Cov.: 32 AF XY: 0.135 AC XY: 9989 AN XY: 74178

African (AFR) AF: 0.211 AC: 8735 AN: 41442

American (AMR) AF: 0.115 AC: 1749 AN: 15204

Ashkenazi Jewish (ASJ) AF: 0.0202 AC: 70 AN: 3464

East Asian (EAS) AF: 0.568 AC: 2892 AN: 5096

South Asian (SAS) AF: 0.229 AC: 1104 AN: 4822

European-Finnish (FIN) AF: 0.114 AC: 1210 AN: 10590

Middle Eastern (MID) AF: 0.0918 AC: 27 AN: 294

European-Non Finnish (NFE) AF: 0.0469 AC: 3184 AN: 67864

Other (OTH) AF: 0.118 AC: 249 AN: 2108

Alfa AF: 0.0732 Hom.: 3929

Bravo AF: 0.131

Asia WGS AF: 0.354 AC: 1228 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.57
DANN	Benign	0.27
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs1037079; hg19: chr4-32590048;