rs4804804

Variant names:

• chr19-7748977-G-A
• rs4804804

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 0.271 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
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.0661 AC: 2746 AN: 41556

American (AMR) AF: 0.279 AC: 4262 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.350 AC: 1214 AN: 3470

East Asian (EAS) AF: 0.449 AC: 2312 AN: 5150

South Asian (SAS) AF: 0.380 AC: 1831 AN: 4818

European-Finnish (FIN) AF: 0.361 AC: 3812 AN: 10552

Middle Eastern (MID) AF: 0.364 AC: 107 AN: 294

European-Non Finnish (NFE) AF: 0.354 AC: 24071 AN: 67950

Other (OTH) AF: 0.292 AC: 616 AN: 2110

Alfa AF: 0.311 Hom.: 2666

Bravo AF: 0.255

Asia WGS AF: 0.352 AC: 1224 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.74
DANN	Benign	0.58
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs4804804; hg19: chr19-7813863;