19-47901208-G-A

Variant names:

• chr19-47901208-G-A
• rs2932760

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 0.231 in 152,084 control chromosomes in the GnomAD database, including 4,875 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 (4875 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.529
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.311 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.232 AC: 35185 AN: 151964 Hom.: 4871 Cov.: 31

Gnomad AFR AF: 0.0760

Gnomad AMI AF: 0.203

Gnomad AMR AF: 0.258

Gnomad ASJ AF: 0.376

Gnomad EAS AF: 0.222

Gnomad SAS AF: 0.323

Gnomad FIN AF: 0.319

Gnomad MID AF: 0.335

Gnomad NFE AF: 0.292

Gnomad OTH AF: 0.274

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

GnomAD4 genome AF: 0.231 AC: 35196 AN: 152084 Hom.: 4875 Cov.: 31 AF XY: 0.236 AC XY: 17510 AN XY: 74312

African (AFR) AF: 0.0759 AC: 3152 AN: 41544

American (AMR) AF: 0.258 AC: 3931 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.376 AC: 1303 AN: 3464

East Asian (EAS) AF: 0.223 AC: 1150 AN: 5164

South Asian (SAS) AF: 0.324 AC: 1560 AN: 4812

European-Finnish (FIN) AF: 0.319 AC: 3370 AN: 10562

Middle Eastern (MID) AF: 0.344 AC: 101 AN: 294

European-Non Finnish (NFE) AF: 0.292 AC: 19864 AN: 67972

Other (OTH) AF: 0.275 AC: 580 AN: 2108

Alfa AF: 0.272 Hom.: 7894

Bravo AF: 0.219

Asia WGS AF: 0.263 AC: 915 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.88
DANN	Benign	0.66
PhyloP100		-0.53

Splicing

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

Other links and lift over

dbSNP: rs2932760; hg19: chr19-48404465;