rs550663

Variant names:

• chr1-48258565-A-G
• rs550663

Your query was ambiguous. Multiple possible variants found:

• chr1-48258565-A-G
• chr1-48258565-A-T

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 0.576 in 152,072 control chromosomes in the GnomAD database, including 26,365 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 0.58 (26365 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.366
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.767 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: 0.576 AC: 87533 AN: 151956 Hom.: 26350 Cov.: 33

Gnomad AFR AF: 0.387

Gnomad AMI AF: 0.656

Gnomad AMR AF: 0.589

Gnomad ASJ AF: 0.700

Gnomad EAS AF: 0.787

Gnomad SAS AF: 0.592

Gnomad FIN AF: 0.642

Gnomad MID AF: 0.604

Gnomad NFE AF: 0.652

Gnomad OTH AF: 0.614

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

GnomAD4 genome AF: 0.576 AC: 87584 AN: 152072 Hom.: 26365 Cov.: 33 AF XY: 0.579 AC XY: 43060 AN XY: 74324

African (AFR) AF: 0.387 AC: 16039 AN: 41474

American (AMR) AF: 0.589 AC: 9002 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.700 AC: 2428 AN: 3468

East Asian (EAS) AF: 0.787 AC: 4067 AN: 5168

South Asian (SAS) AF: 0.591 AC: 2852 AN: 4828

European-Finnish (FIN) AF: 0.642 AC: 6782 AN: 10568

Middle Eastern (MID) AF: 0.612 AC: 180 AN: 294

European-Non Finnish (NFE) AF: 0.652 AC: 44334 AN: 67974

Other (OTH) AF: 0.616 AC: 1303 AN: 2116

Alfa AF: 0.615 Hom.: 3668

Bravo AF: 0.565

Asia WGS AF: 0.691 AC: 2401 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	4.2
DANN	Benign	0.50
PhyloP100		0.37

Splicing

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

Other links and lift over

dbSNP: rs550663; hg19: chr1-48724237;