rs6550825

chr3-23993478-G-A

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 0.599 in 151,050 control chromosomes in the GnomAD database, including 27,866 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 0.60 (27866 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0760

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.683 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: 0.599 AC: 90384 AN: 150940 Hom.: 27843 Cov.: 29

Gnomad AFR AF: 0.447

Gnomad AMI AF: 0.485

Gnomad AMR AF: 0.628

Gnomad ASJ AF: 0.710

Gnomad EAS AF: 0.481

Gnomad SAS AF: 0.606

Gnomad FIN AF: 0.592

Gnomad MID AF: 0.728

Gnomad NFE AF: 0.689

Gnomad OTH AF: 0.625

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

GnomAD4 genome AF: 0.599 AC: 90449 AN: 151050 Hom.: 27866 Cov.: 29 AF XY: 0.596 AC XY: 43954 AN XY: 73746

Gnomad4 AFR AF: 0.447

Gnomad4 AMR AF: 0.628

Gnomad4 ASJ AF: 0.710

Gnomad4 EAS AF: 0.481

Gnomad4 SAS AF: 0.606

Gnomad4 FIN AF: 0.592

Gnomad4 NFE AF: 0.689

Gnomad4 OTH AF: 0.623

Alfa AF: 0.673 Hom.: 41692

Bravo AF: 0.595

Asia WGS AF: 0.546 AC: 1899 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
Cadd	Benign	0.53
Dann	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6550825; hg19: chr3-24034969;