19-49049398-A-G

Variant names:

• chr19-49049398-A-G
• rs4801790

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 0.311 in 147,528 control chromosomes in the GnomAD database, including 7,520 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 0.31 (7520 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0230
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.355 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: 0.311 AC: 45895 AN: 147424 Hom.: 7508 Cov.: 31

Gnomad AFR AF: 0.350

Gnomad AMI AF: 0.264

Gnomad AMR AF: 0.363

Gnomad ASJ AF: 0.310

Gnomad EAS AF: 0.149

Gnomad SAS AF: 0.314

Gnomad FIN AF: 0.213

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.307

Gnomad OTH AF: 0.312

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

GnomAD4 genome AF: 0.311 AC: 45938 AN: 147528 Hom.: 7520 Cov.: 31 AF XY: 0.309 AC XY: 22270 AN XY: 72072

African (AFR) AF: 0.351 AC: 13105 AN: 37370

American (AMR) AF: 0.363 AC: 5473 AN: 15076

Ashkenazi Jewish (ASJ) AF: 0.310 AC: 1077 AN: 3470

East Asian (EAS) AF: 0.149 AC: 766 AN: 5156

South Asian (SAS) AF: 0.314 AC: 1509 AN: 4804

European-Finnish (FIN) AF: 0.213 AC: 2242 AN: 10550

Middle Eastern (MID) AF: 0.255 AC: 74 AN: 290

European-Non Finnish (NFE) AF: 0.307 AC: 20814 AN: 67838

Other (OTH) AF: 0.309 AC: 638 AN: 2064

Alfa AF: 0.310 Hom.: 901

Bravo AF: 0.326

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	4.1
DANN	Benign	0.080
PhyloP100		0.023
PromoterAI		0.010	Neutral

Splicing

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

Other links and lift over

dbSNP: rs4801790; hg19: chr19-49552655;