rs4804805

Variant names:

• chr19-7751660-A-G
• rs4804805

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 0.232 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.232 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

Gnomad4 AFR AF: 0.0785

Gnomad4 AMR AF: 0.257

Gnomad4 ASJ AF: 0.263

Gnomad4 EAS AF: 0.0860

Gnomad4 SAS AF: 0.239

Gnomad4 FIN AF: 0.270

Gnomad4 NFE AF: 0.321

Gnomad4 OTH AF: 0.258

Alfa AF: 0.305 Hom.: 10482

Bravo AF: 0.223

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4804805; hg19: chr19-7816546;