rs4801789

Positions:

• chr19-49043554-T-C

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 0.353 in 120,728 control chromosomes in the GnomAD database, including 5,484 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 0.35 (5484 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.817

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.414 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: 0.353 AC: 42612 AN: 120626 Hom.: 5477 Cov.: 33

Gnomad AFR AF: 0.394

Gnomad AMI AF: 0.327

Gnomad AMR AF: 0.423

Gnomad ASJ AF: 0.387

Gnomad EAS AF: 0.182

Gnomad SAS AF: 0.365

Gnomad FIN AF: 0.255

Gnomad MID AF: 0.320

Gnomad NFE AF: 0.338

Gnomad OTH AF: 0.357

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

GnomAD4 genome AF: 0.353 AC: 42648 AN: 120728 Hom.: 5484 Cov.: 33 AF XY: 0.353 AC XY: 20756 AN XY: 58804

Gnomad4 AFR AF: 0.394

Gnomad4 AMR AF: 0.424

Gnomad4 ASJ AF: 0.387

Gnomad4 EAS AF: 0.181

Gnomad4 SAS AF: 0.366

Gnomad4 FIN AF: 0.255

Gnomad4 NFE AF: 0.338

Gnomad4 OTH AF: 0.353

Alfa AF: 0.339 Hom.: 564

Asia WGS AF: 0.302 AC: 1052 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	1.8
DANN	Benign	0.14

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4801789; hg19: chr19-49546811; COSMIC: COSV56823433;