rs6550825

Variant names:

• chr3-23993478-G-A
• rs6550825

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.447 AC: 18414 AN: 41176

American (AMR) AF: 0.628 AC: 9549 AN: 15204

Ashkenazi Jewish (ASJ) AF: 0.710 AC: 2455 AN: 3460

East Asian (EAS) AF: 0.481 AC: 2469 AN: 5130

South Asian (SAS) AF: 0.606 AC: 2905 AN: 4792

European-Finnish (FIN) AF: 0.592 AC: 6104 AN: 10314

Middle Eastern (MID) AF: 0.721 AC: 209 AN: 290

European-Non Finnish (NFE) AF: 0.689 AC: 46595 AN: 67674

Other (OTH) AF: 0.623 AC: 1309 AN: 2102

Alfa AF: 0.659 Hom.: 113948

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
PhyloP100		0.076

Splicing

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

Other links and lift over

dbSNP: rs6550825; hg19: chr3-24034969;