rs4806907

Variant names:

• chr19-3093165-T-C
• rs4806907

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 0.38 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
• Publications: 12 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.294 AC: 12176 AN: 41480

American (AMR) AF: 0.368 AC: 5629 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.421 AC: 1461 AN: 3468

East Asian (EAS) AF: 0.385 AC: 1986 AN: 5160

South Asian (SAS) AF: 0.339 AC: 1635 AN: 4822

European-Finnish (FIN) AF: 0.355 AC: 3749 AN: 10564

Middle Eastern (MID) AF: 0.354 AC: 104 AN: 294

European-Non Finnish (NFE) AF: 0.440 AC: 29894 AN: 67972

Other (OTH) AF: 0.377 AC: 796 AN: 2110

Alfa AF: 0.407 Hom.: 21627

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
PhyloP100		-0.71

Splicing

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

Other links and lift over

dbSNP: rs4806907; hg19: chr19-3093163;