chr19-10957972-C-A

Variant names:

• chr19-10957972-C-A
• rs1019935

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.387 AC: 15991 AN: 41328

American (AMR) AF: 0.350 AC: 5326 AN: 15220

Ashkenazi Jewish (ASJ) AF: 0.430 AC: 1489 AN: 3460

East Asian (EAS) AF: 0.309 AC: 1567 AN: 5064

South Asian (SAS) AF: 0.479 AC: 2297 AN: 4798

European-Finnish (FIN) AF: 0.388 AC: 4085 AN: 10518

Middle Eastern (MID) AF: 0.469 AC: 137 AN: 292

European-Non Finnish (NFE) AF: 0.409 AC: 27774 AN: 67862

Other (OTH) AF: 0.393 AC: 830 AN: 2110

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
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs1019935; hg19: chr19-11068648;