rs4802189

Positions:

• chr19-43642778-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 0.202 in 152,138 control chromosomes in the GnomAD database, including 3,337 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 0.20 (3337 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.257

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.265 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: 0.202 AC: 30650 AN: 152020 Hom.: 3333 Cov.: 32

Gnomad AFR AF: 0.269

Gnomad AMI AF: 0.101

Gnomad AMR AF: 0.252

Gnomad ASJ AF: 0.161

Gnomad EAS AF: 0.105

Gnomad SAS AF: 0.0964

Gnomad FIN AF: 0.137

Gnomad MID AF: 0.335

Gnomad NFE AF: 0.177

Gnomad OTH AF: 0.218

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

GnomAD4 genome AF: 0.202 AC: 30674 AN: 152138 Hom.: 3337 Cov.: 32 AF XY: 0.200 AC XY: 14844 AN XY: 74370

Gnomad4 AFR AF: 0.269

Gnomad4 AMR AF: 0.252

Gnomad4 ASJ AF: 0.161

Gnomad4 EAS AF: 0.104

Gnomad4 SAS AF: 0.0968

Gnomad4 FIN AF: 0.137

Gnomad4 NFE AF: 0.177

Gnomad4 OTH AF: 0.217

Alfa AF: 0.191 Hom.: 3278

Bravo AF: 0.219

Asia WGS AF: 0.133 AC: 462 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	9.9
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4802189; hg19: chr19-44146930;