rs2870529

Positions:

• chr19-28759663-T-A

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;