rs2870529

Variant names:

• chr19-28759663-T-A
• rs2870529

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 0.325 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.325 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

Gnomad4 AFR AF: 0.173

Gnomad4 AMR AF: 0.396

Gnomad4 ASJ AF: 0.309

Gnomad4 EAS AF: 0.104

Gnomad4 SAS AF: 0.207

Gnomad4 FIN AF: 0.366

Gnomad4 NFE AF: 0.420

Gnomad4 OTH AF: 0.340

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2870529; hg19: chr19-29250570;