rs4806907

Positions:

• chr19-3093165-T-C

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 0.38 in 152,064 control chromosomes in the GnomAD database, including 11,412 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 0.38 (11412 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.706

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.436 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: 0.380 AC: 57716 AN: 151946 Hom.: 11397 Cov.: 32

Gnomad AFR AF: 0.293

Gnomad AMI AF: 0.375

Gnomad AMR AF: 0.369

Gnomad ASJ AF: 0.421

Gnomad EAS AF: 0.384

Gnomad SAS AF: 0.339

Gnomad FIN AF: 0.355

Gnomad MID AF: 0.358

Gnomad NFE AF: 0.440

Gnomad OTH AF: 0.373

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

GnomAD4 genome AF: 0.380 AC: 57772 AN: 152064 Hom.: 11412 Cov.: 32 AF XY: 0.374 AC XY: 27817 AN XY: 74308

Gnomad4 AFR AF: 0.294

Gnomad4 AMR AF: 0.368

Gnomad4 ASJ AF: 0.421

Gnomad4 EAS AF: 0.385

Gnomad4 SAS AF: 0.339

Gnomad4 FIN AF: 0.355

Gnomad4 NFE AF: 0.440

Gnomad4 OTH AF: 0.377

Alfa AF: 0.410 Hom.: 15558

Bravo AF: 0.378

Asia WGS AF: 0.372 AC: 1294 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.60
DANN	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4806907; hg19: chr19-3093163;