rs4857855

Variant names:

• chr3-128541707-C-T
• rs4857855

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 0.184 in 152,074 control chromosomes in the GnomAD database, including 2,839 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 0.18 (2839 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.282
• Publications: 28 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.332 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: 0.184 AC: 27968 AN: 151954 Hom.: 2833 Cov.: 31

Gnomad AFR AF: 0.135

Gnomad AMI AF: 0.221

Gnomad AMR AF: 0.221

Gnomad ASJ AF: 0.245

Gnomad EAS AF: 0.346

Gnomad SAS AF: 0.239

Gnomad FIN AF: 0.205

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.183

Gnomad OTH AF: 0.176

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

GnomAD4 genome AF: 0.184 AC: 27985 AN: 152074 Hom.: 2839 Cov.: 31 AF XY: 0.188 AC XY: 13983 AN XY: 74342

African (AFR) AF: 0.135 AC: 5605 AN: 41482

American (AMR) AF: 0.221 AC: 3381 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.245 AC: 849 AN: 3464

East Asian (EAS) AF: 0.345 AC: 1781 AN: 5158

South Asian (SAS) AF: 0.239 AC: 1150 AN: 4814

European-Finnish (FIN) AF: 0.205 AC: 2170 AN: 10586

Middle Eastern (MID) AF: 0.187 AC: 55 AN: 294

European-Non Finnish (NFE) AF: 0.183 AC: 12417 AN: 67986

Other (OTH) AF: 0.179 AC: 376 AN: 2104

Alfa AF: 0.187 Hom.: 13257

Bravo AF: 0.186

Asia WGS AF: 0.252 AC: 876 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.3
DANN	Benign	0.38
PhyloP100		0.28

Splicing

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

Other links and lift over

dbSNP: rs4857855; hg19: chr3-128260550;