rs4805877

Variant names:

• chr19-33385488-A-G
• rs4805877

Your query was ambiguous. Multiple possible variants found:

• chr19-33385488-A-G
• chr19-33385488-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 0.485 in 152,130 control chromosomes in the GnomAD database, including 18,999 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 0.48 (18999 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00900
• Publications: 14 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.661 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: 0.485 AC: 73705 AN: 152012 Hom.: 18971 Cov.: 33

Gnomad AFR AF: 0.668

Gnomad AMI AF: 0.429

Gnomad AMR AF: 0.454

Gnomad ASJ AF: 0.358

Gnomad EAS AF: 0.372

Gnomad SAS AF: 0.370

Gnomad FIN AF: 0.474

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.407

Gnomad OTH AF: 0.475

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

GnomAD4 genome AF: 0.485 AC: 73775 AN: 152130 Hom.: 18999 Cov.: 33 AF XY: 0.485 AC XY: 36094 AN XY: 74378

African (AFR) AF: 0.668 AC: 27712 AN: 41512

American (AMR) AF: 0.455 AC: 6950 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.358 AC: 1240 AN: 3468

East Asian (EAS) AF: 0.372 AC: 1927 AN: 5180

South Asian (SAS) AF: 0.370 AC: 1785 AN: 4826

European-Finnish (FIN) AF: 0.474 AC: 5009 AN: 10558

Middle Eastern (MID) AF: 0.391 AC: 115 AN: 294

European-Non Finnish (NFE) AF: 0.407 AC: 27652 AN: 67980

Other (OTH) AF: 0.470 AC: 994 AN: 2114

Alfa AF: 0.424 Hom.: 28502

Bravo AF: 0.494

Asia WGS AF: 0.378 AC: 1318 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	3.4
DANN	Benign	0.77
PhyloP100		0.0090

Splicing

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

Other links and lift over

dbSNP: rs4805877; hg19: chr19-33876394;