rs6550825

Variant names:

• chr3-23993478-G-A
• rs6550825

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;