rs4803750

chr19-44744370-A-G

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 0.0779 in 151,814 control chromosomes in the GnomAD database, including 548 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 0.078 (548 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.243

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.148 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0779 AC: 11823 AN: 151714 Hom.: 547 Cov.: 32

Gnomad AFR AF: 0.0801

Gnomad AMI AF: 0.0253

Gnomad AMR AF: 0.125

Gnomad ASJ AF: 0.0985

Gnomad EAS AF: 0.0730

Gnomad SAS AF: 0.158

Gnomad FIN AF: 0.0521

Gnomad MID AF: 0.0541

Gnomad NFE AF: 0.0648

Gnomad OTH AF: 0.0653

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

GnomAD4 genome AF: 0.0779 AC: 11830 AN: 151814 Hom.: 548 Cov.: 32 AF XY: 0.0784 AC XY: 5816 AN XY: 74198

Gnomad4 AFR AF: 0.0802

Gnomad4 AMR AF: 0.125

Gnomad4 ASJ AF: 0.0985

Gnomad4 EAS AF: 0.0728

Gnomad4 SAS AF: 0.157

Gnomad4 FIN AF: 0.0521

Gnomad4 NFE AF: 0.0648

Gnomad4 OTH AF: 0.0657

Alfa AF: 0.0789 Hom.: 304

Bravo AF: 0.0836

Asia WGS AF: 0.112 AC: 389 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
Cadd	Benign	0.80
Dann	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4803750; hg19: chr19-45247627;