rs4802307

Variant names:

• chr19-46346549-G-T
• rs4802307

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 62 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.0920 AC: 3818 AN: 41502

American (AMR) AF: 0.210 AC: 3213 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.255 AC: 884 AN: 3466

East Asian (EAS) AF: 0.0426 AC: 220 AN: 5160

South Asian (SAS) AF: 0.127 AC: 610 AN: 4820

European-Finnish (FIN) AF: 0.227 AC: 2395 AN: 10560

Middle Eastern (MID) AF: 0.264 AC: 77 AN: 292

European-Non Finnish (NFE) AF: 0.299 AC: 20310 AN: 67952

Other (OTH) AF: 0.229 AC: 480 AN: 2098

Alfa AF: 0.259 Hom.: 11687

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
PhyloP100		-0.098

Splicing

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

Other links and lift over

dbSNP: rs4802307; hg19: chr19-46849806;