rs4804806

Variant names:

• chr19-7751739-G-A
• rs4804806

Your query was ambiguous. Multiple possible variants found:

• chr19-7751739-G-A
• chr19-7751739-G-C

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 0.355 in 152,086 control chromosomes in the GnomAD database, including 9,893 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 0.36 (9893 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.90
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.41 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: 0.355 AC: 53942 AN: 151968 Hom.: 9876 Cov.: 32

Gnomad AFR AF: 0.363

Gnomad AMI AF: 0.475

Gnomad AMR AF: 0.419

Gnomad ASJ AF: 0.372

Gnomad EAS AF: 0.135

Gnomad SAS AF: 0.202

Gnomad FIN AF: 0.317

Gnomad MID AF: 0.446

Gnomad NFE AF: 0.365

Gnomad OTH AF: 0.388

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

GnomAD4 genome AF: 0.355 AC: 53997 AN: 152086 Hom.: 9893 Cov.: 32 AF XY: 0.351 AC XY: 26124 AN XY: 74362

African (AFR) AF: 0.363 AC: 15067 AN: 41486

American (AMR) AF: 0.419 AC: 6398 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.372 AC: 1291 AN: 3470

East Asian (EAS) AF: 0.136 AC: 701 AN: 5168

South Asian (SAS) AF: 0.202 AC: 975 AN: 4828

European-Finnish (FIN) AF: 0.317 AC: 3349 AN: 10580

Middle Eastern (MID) AF: 0.442 AC: 129 AN: 292

European-Non Finnish (NFE) AF: 0.365 AC: 24834 AN: 67968

Other (OTH) AF: 0.389 AC: 821 AN: 2110

Alfa AF: 0.364 Hom.: 18227

Bravo AF: 0.367

Asia WGS AF: 0.201 AC: 701 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.17
DANN	Benign	0.15
PhyloP100		-2.9

Splicing

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

Other links and lift over

dbSNP: rs4804806; hg19: chr19-7816625;