rs4803413

Variant names:

• chr19-40980072-G-A
• rs4803413

Your query was ambiguous. Multiple possible variants found:

• chr19-40980072-G-A
• chr19-40980072-G-C
• chr19-40980072-G-T

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 0.298 in 151,874 control chromosomes in the GnomAD database, including 7,637 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 0.30 (7637 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.252
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.445 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: 0.298 AC: 45262 AN: 151756 Hom.: 7638 Cov.: 31

Gnomad AFR AF: 0.148

Gnomad AMI AF: 0.293

Gnomad AMR AF: 0.361

Gnomad ASJ AF: 0.322

Gnomad EAS AF: 0.460

Gnomad SAS AF: 0.350

Gnomad FIN AF: 0.435

Gnomad MID AF: 0.385

Gnomad NFE AF: 0.336

Gnomad OTH AF: 0.303

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

GnomAD4 genome AF: 0.298 AC: 45278 AN: 151874 Hom.: 7637 Cov.: 31 AF XY: 0.305 AC XY: 22633 AN XY: 74224

African (AFR) AF: 0.148 AC: 6135 AN: 41374

American (AMR) AF: 0.362 AC: 5522 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.322 AC: 1118 AN: 3470

East Asian (EAS) AF: 0.461 AC: 2372 AN: 5148

South Asian (SAS) AF: 0.350 AC: 1681 AN: 4806

European-Finnish (FIN) AF: 0.435 AC: 4583 AN: 10546

Middle Eastern (MID) AF: 0.387 AC: 113 AN: 292

European-Non Finnish (NFE) AF: 0.336 AC: 22849 AN: 67956

Other (OTH) AF: 0.303 AC: 639 AN: 2110

Alfa AF: 0.205 Hom.: 507

Bravo AF: 0.288

Asia WGS AF: 0.374 AC: 1303 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.6
DANN	Benign	0.56
PhyloP100		0.25

Splicing

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

Other links and lift over

dbSNP: rs4803413; hg19: chr19-41485977;