rs4804805

Variant names:

• chr19-7751660-A-G
• rs4804805

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 0.232 in 152,188 control chromosomes in the GnomAD database, including 5,010 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 0.23 (5010 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.164
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.318 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: 0.232 AC: 35286 AN: 152070 Hom.: 5012 Cov.: 32

Gnomad AFR AF: 0.0787

Gnomad AMI AF: 0.284

Gnomad AMR AF: 0.257

Gnomad ASJ AF: 0.263

Gnomad EAS AF: 0.0858

Gnomad SAS AF: 0.239

Gnomad FIN AF: 0.270

Gnomad MID AF: 0.347

Gnomad NFE AF: 0.321

Gnomad OTH AF: 0.259

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

GnomAD4 genome AF: 0.232 AC: 35280 AN: 152188 Hom.: 5010 Cov.: 32 AF XY: 0.228 AC XY: 16957 AN XY: 74402

African (AFR) AF: 0.0785 AC: 3262 AN: 41554

American (AMR) AF: 0.257 AC: 3926 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.263 AC: 914 AN: 3470

East Asian (EAS) AF: 0.0860 AC: 446 AN: 5186

South Asian (SAS) AF: 0.239 AC: 1154 AN: 4820

European-Finnish (FIN) AF: 0.270 AC: 2857 AN: 10598

Middle Eastern (MID) AF: 0.339 AC: 99 AN: 292

European-Non Finnish (NFE) AF: 0.321 AC: 21819 AN: 67950

Other (OTH) AF: 0.258 AC: 544 AN: 2112

Alfa AF: 0.294 Hom.: 13523

Bravo AF: 0.223

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	5.3
DANN	Benign	0.68
PhyloP100		0.16

Splicing

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

Other links and lift over

dbSNP: rs4804805; hg19: chr19-7816546;