19-28759663-T-A

Variant names:

• chr19-28759663-T-A
• rs2870529

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 0.325 in 152,018 control chromosomes in the GnomAD database, including 9,036 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 0.32 (9036 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.106
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.416 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: 0.325 AC: 49336 AN: 151900 Hom.: 9037 Cov.: 32

Gnomad AFR AF: 0.173

Gnomad AMI AF: 0.341

Gnomad AMR AF: 0.396

Gnomad ASJ AF: 0.309

Gnomad EAS AF: 0.104

Gnomad SAS AF: 0.207

Gnomad FIN AF: 0.366

Gnomad MID AF: 0.301

Gnomad NFE AF: 0.420

Gnomad OTH AF: 0.344

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

GnomAD4 genome AF: 0.325 AC: 49335 AN: 152018 Hom.: 9036 Cov.: 32 AF XY: 0.322 AC XY: 23924 AN XY: 74298

African (AFR) AF: 0.173 AC: 7167 AN: 41498

American (AMR) AF: 0.396 AC: 6041 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.309 AC: 1069 AN: 3464

East Asian (EAS) AF: 0.104 AC: 536 AN: 5166

South Asian (SAS) AF: 0.207 AC: 998 AN: 4810

European-Finnish (FIN) AF: 0.366 AC: 3862 AN: 10550

Middle Eastern (MID) AF: 0.306 AC: 90 AN: 294

European-Non Finnish (NFE) AF: 0.420 AC: 28545 AN: 67946

Other (OTH) AF: 0.340 AC: 717 AN: 2108

Alfa AF: 0.370 Hom.: 1364

Bravo AF: 0.320

Asia WGS AF: 0.145 AC: 505 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	3.4
DANN	Benign	0.20
PhyloP100		0.11

Splicing

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

Other links and lift over

dbSNP: rs2870529; hg19: chr19-29250570;