rs6550139

Positions:

• chr3-32591577-A-T

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;