rs4804804

Variant names:

• chr19-7748977-G-A
• rs4804804

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 0.271 in 152,094 control chromosomes in the GnomAD database, including 6,905 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 0.27 (6905 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.66

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.434 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: 0.271 AC: 41225 AN: 151976 Hom.: 6901 Cov.: 32

Gnomad AFR AF: 0.0663

Gnomad AMI AF: 0.284

Gnomad AMR AF: 0.279

Gnomad ASJ AF: 0.350

Gnomad EAS AF: 0.449

Gnomad SAS AF: 0.379

Gnomad FIN AF: 0.361

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.354

Gnomad OTH AF: 0.292

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

GnomAD4 genome AF: 0.271 AC: 41230 AN: 152094 Hom.: 6905 Cov.: 32 AF XY: 0.275 AC XY: 20471 AN XY: 74344

Gnomad4 AFR AF: 0.0661

Gnomad4 AMR AF: 0.279

Gnomad4 ASJ AF: 0.350

Gnomad4 EAS AF: 0.449

Gnomad4 SAS AF: 0.380

Gnomad4 FIN AF: 0.361

Gnomad4 NFE AF: 0.354

Gnomad4 OTH AF: 0.292

Alfa AF: 0.295 Hom.: 1164

Bravo AF: 0.255

Asia WGS AF: 0.352 AC: 1224 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.74
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4804804; hg19: chr19-7813863;