rs4803595

Variant names:

• chr19-43290001-T-A
• rs4803595

Your query was ambiguous. Multiple possible variants found:

• chr19-43290001-T-A
• chr19-43290001-T-G

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 0.28 in 152,064 control chromosomes in the GnomAD database, including 6,318 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 0.28 (6318 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.146
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.327 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: 0.280 AC: 42591 AN: 151946 Hom.: 6315 Cov.: 32

Gnomad AFR AF: 0.213

Gnomad AMI AF: 0.246

Gnomad AMR AF: 0.271

Gnomad ASJ AF: 0.294

Gnomad EAS AF: 0.294

Gnomad SAS AF: 0.148

Gnomad FIN AF: 0.286

Gnomad MID AF: 0.207

Gnomad NFE AF: 0.331

Gnomad OTH AF: 0.277

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

GnomAD4 genome AF: 0.280 AC: 42618 AN: 152064 Hom.: 6318 Cov.: 32 AF XY: 0.275 AC XY: 20420 AN XY: 74344

African (AFR) AF: 0.213 AC: 8845 AN: 41482

American (AMR) AF: 0.271 AC: 4140 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.294 AC: 1017 AN: 3464

East Asian (EAS) AF: 0.294 AC: 1525 AN: 5182

South Asian (SAS) AF: 0.148 AC: 713 AN: 4814

European-Finnish (FIN) AF: 0.286 AC: 3020 AN: 10568

Middle Eastern (MID) AF: 0.219 AC: 64 AN: 292

European-Non Finnish (NFE) AF: 0.331 AC: 22487 AN: 67948

Other (OTH) AF: 0.276 AC: 583 AN: 2112

Alfa AF: 0.320 Hom.: 1012

Bravo AF: 0.277

Asia WGS AF: 0.222 AC: 770 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	7.1
DANN	Benign	0.42
PhyloP100		0.15

Splicing

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

Other links and lift over

dbSNP: rs4803595; hg19: chr19-43794153;