19-33562965-C-T

Variant names:

• chr19-33562965-C-T
• rs12972735

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 0.429 in 152,042 control chromosomes in the GnomAD database, including 14,188 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 0.43 (14188 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.263

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.498 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: 0.429 AC: 65201 AN: 151922 Hom.: 14169 Cov.: 32

Gnomad AFR AF: 0.504

Gnomad AMI AF: 0.441

Gnomad AMR AF: 0.454

Gnomad ASJ AF: 0.432

Gnomad EAS AF: 0.431

Gnomad SAS AF: 0.370

Gnomad FIN AF: 0.436

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.381

Gnomad OTH AF: 0.437

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

GnomAD4 genome AF: 0.429 AC: 65266 AN: 152042 Hom.: 14188 Cov.: 32 AF XY: 0.432 AC XY: 32150 AN XY: 74350

Gnomad4 AFR AF: 0.504

Gnomad4 AMR AF: 0.454

Gnomad4 ASJ AF: 0.432

Gnomad4 EAS AF: 0.430

Gnomad4 SAS AF: 0.370

Gnomad4 FIN AF: 0.436

Gnomad4 NFE AF: 0.381

Gnomad4 OTH AF: 0.437

Alfa AF: 0.384 Hom.: 12026

Bravo AF: 0.436

Asia WGS AF: 0.413 AC: 1441 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.4
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12972735; hg19: chr19-34053871;