rs1019935

Positions:

• chr19-10957972-C-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 0.395 in 151,550 control chromosomes in the GnomAD database, including 11,854 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 0.39 (11854 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.47

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.462 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.394 AC: 59739 AN: 151432 Hom.: 11819 Cov.: 30

Gnomad AFR AF: 0.386

Gnomad AMI AF: 0.376

Gnomad AMR AF: 0.350

Gnomad ASJ AF: 0.430

Gnomad EAS AF: 0.309

Gnomad SAS AF: 0.478

Gnomad FIN AF: 0.388

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.409

Gnomad OTH AF: 0.392

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

GnomAD4 genome AF: 0.395 AC: 59834 AN: 151550 Hom.: 11854 Cov.: 30 AF XY: 0.394 AC XY: 29180 AN XY: 74046

Gnomad4 AFR AF: 0.387

Gnomad4 AMR AF: 0.350

Gnomad4 ASJ AF: 0.430

Gnomad4 EAS AF: 0.309

Gnomad4 SAS AF: 0.479

Gnomad4 FIN AF: 0.388

Gnomad4 NFE AF: 0.409

Gnomad4 OTH AF: 0.393

Alfa AF: 0.390 Hom.: 1417

Bravo AF: 0.390

Asia WGS AF: 0.411 AC: 1428 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.28
DANN	Benign	0.24

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1019935; hg19: chr19-11068648;