rs6550139

Variant names:

• chr3-32591577-A-T
• rs6550139

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

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: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.591

ACMG classification

Verdict is Benign. Variant got -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

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

Gnomad4 AFR AF: 0.556

Gnomad4 AMR AF: 0.463

Gnomad4 ASJ AF: 0.568

Gnomad4 EAS AF: 0.515

Gnomad4 SAS AF: 0.464

Gnomad4 FIN AF: 0.464

Gnomad4 NFE AF: 0.515

Gnomad4 OTH AF: 0.503

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6550139; hg19: chr3-32633069;