rs958039

Positions:

• chr19-39239661-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 0.357 in 151,918 control chromosomes in the GnomAD database, including 10,464 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 0.36 (10464 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.841

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.485 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: 0.357 AC: 54139 AN: 151798 Hom.: 10441 Cov.: 31

Gnomad AFR AF: 0.491

Gnomad AMI AF: 0.367

Gnomad AMR AF: 0.365

Gnomad ASJ AF: 0.408

Gnomad EAS AF: 0.0821

Gnomad SAS AF: 0.233

Gnomad FIN AF: 0.248

Gnomad MID AF: 0.345

Gnomad NFE AF: 0.318

Gnomad OTH AF: 0.343

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

GnomAD4 genome AF: 0.357 AC: 54215 AN: 151918 Hom.: 10464 Cov.: 31 AF XY: 0.350 AC XY: 25946 AN XY: 74236

Gnomad4 AFR AF: 0.491

Gnomad4 AMR AF: 0.365

Gnomad4 ASJ AF: 0.408

Gnomad4 EAS AF: 0.0825

Gnomad4 SAS AF: 0.233

Gnomad4 FIN AF: 0.248

Gnomad4 NFE AF: 0.318

Gnomad4 OTH AF: 0.340

Alfa AF: 0.354 Hom.: 1215

Bravo AF: 0.372

Asia WGS AF: 0.201 AC: 704 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.6
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs958039; hg19: chr19-39730301;