rs2739493

Variant names:

• chr19-50897420-A-C
• rs2739493

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 0.495 in 151,482 control chromosomes in the GnomAD database, including 20,208 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 0.50 (20208 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.48

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.709 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: 0.495 AC: 74946 AN: 151364 Hom.: 20168 Cov.: 31

Gnomad AFR AF: 0.715

Gnomad AMI AF: 0.501

Gnomad AMR AF: 0.419

Gnomad ASJ AF: 0.428

Gnomad EAS AF: 0.212

Gnomad SAS AF: 0.497

Gnomad FIN AF: 0.345

Gnomad MID AF: 0.598

Gnomad NFE AF: 0.426

Gnomad OTH AF: 0.507

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

GnomAD4 genome AF: 0.495 AC: 75039 AN: 151482 Hom.: 20208 Cov.: 31 AF XY: 0.489 AC XY: 36175 AN XY: 73970

Gnomad4 AFR AF: 0.715

Gnomad4 AMR AF: 0.418

Gnomad4 ASJ AF: 0.428

Gnomad4 EAS AF: 0.212

Gnomad4 SAS AF: 0.496

Gnomad4 FIN AF: 0.345

Gnomad4 NFE AF: 0.425

Gnomad4 OTH AF: 0.509

Alfa AF: 0.218 Hom.: 404

Bravo AF: 0.505

Asia WGS AF: 0.397 AC: 1382 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.5
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2739493; hg19: chr19-51400676;