rs6550139

Variant names:

• chr3-32591577-A-T
• rs6550139
• ENST00000799153.1:n.437-2432A>T

Variant summary

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

The ENST00000799153.1(ENSG00000304056):​n.437-2432A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.516 in 151,924 control chromosomes in the GnomAD database, including 20,334 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 0.52 (20334 hom., cov: 31)
• Consequence: ENSG00000304056 ENST00000799153.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.591
• Publications: 2 publications found

Genes affected

ENSG00000304056 (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 = 0.55 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
ENSG00000304056	ENST00000799153.1	n.437-2432A>T		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes AF: 0.516 AC: 78366 AN: 151804 Hom.: 20320 Cov.: 31

Gnomad AFR AF: 0.555

Gnomad AMI AF: 0.452

Gnomad AMR AF: 0.462

Gnomad ASJ AF: 0.568

Gnomad EAS AF: 0.516

Gnomad SAS AF: 0.464

Gnomad FIN AF: 0.464

Gnomad MID AF: 0.538

Gnomad NFE AF: 0.515

Gnomad OTH AF: 0.506

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

GnomAD4 genome AF: 0.516 AC: 78434 AN: 151924 Hom.: 20334 Cov.: 31 AF XY: 0.511 AC XY: 37970 AN XY: 74240

African (AFR) AF: 0.556 AC: 23013 AN: 41424

American (AMR) AF: 0.463 AC: 7062 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.568 AC: 1970 AN: 3470

East Asian (EAS) AF: 0.515 AC: 2666 AN: 5172

South Asian (SAS) AF: 0.464 AC: 2239 AN: 4824

European-Finnish (FIN) AF: 0.464 AC: 4887 AN: 10522

Middle Eastern (MID) AF: 0.541 AC: 159 AN: 294

European-Non Finnish (NFE) AF: 0.515 AC: 34969 AN: 67942

Other (OTH) AF: 0.503 AC: 1058 AN: 2104

Alfa AF: 0.517 Hom.: 2571

Bravo AF: 0.520

Asia WGS AF: 0.466 AC: 1622 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.0
DANN	Benign	0.62
PhyloP100		-0.59

Splicing

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

Other links and lift over

dbSNP: rs6550139; hg19: chr3-32633069;