rs4802307

Variant names:

• chr19-46346549-G-T
• rs4802307

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 0.212 in 152,032 control chromosomes in the GnomAD database, including 4,101 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 0.21 (4101 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0980

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.295 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: 0.213 AC: 32307 AN: 151914 Hom.: 4106 Cov.: 31

Gnomad AFR AF: 0.0922

Gnomad AMI AF: 0.316

Gnomad AMR AF: 0.211

Gnomad ASJ AF: 0.255

Gnomad EAS AF: 0.0425

Gnomad SAS AF: 0.128

Gnomad FIN AF: 0.227

Gnomad MID AF: 0.268

Gnomad NFE AF: 0.299

Gnomad OTH AF: 0.230

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

GnomAD4 genome AF: 0.212 AC: 32295 AN: 152032 Hom.: 4101 Cov.: 31 AF XY: 0.208 AC XY: 15428 AN XY: 74310

Gnomad4 AFR AF: 0.0920

Gnomad4 AMR AF: 0.210

Gnomad4 ASJ AF: 0.255

Gnomad4 EAS AF: 0.0426

Gnomad4 SAS AF: 0.127

Gnomad4 FIN AF: 0.227

Gnomad4 NFE AF: 0.299

Gnomad4 OTH AF: 0.229

Alfa AF: 0.281 Hom.: 7871

Bravo AF: 0.209

Asia WGS AF: 0.0950 AC: 330 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	2.0
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4802307; hg19: chr19-46849806;