rs4128208

Variant names:

• chr18-51268450-C-A
• rs4128208

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 0.103 in 152,214 control chromosomes in the GnomAD database, including 1,044 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 0.10 (1044 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.35
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.196 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: 0.103 AC: 15617 AN: 152096 Hom.: 1043 Cov.: 33

Gnomad AFR AF: 0.0298

Gnomad AMI AF: 0.133

Gnomad AMR AF: 0.139

Gnomad ASJ AF: 0.167

Gnomad EAS AF: 0.110

Gnomad SAS AF: 0.207

Gnomad FIN AF: 0.114

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.125

Gnomad OTH AF: 0.113

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

GnomAD4 genome AF: 0.103 AC: 15615 AN: 152214 Hom.: 1044 Cov.: 33 AF XY: 0.105 AC XY: 7795 AN XY: 74410

African (AFR) AF: 0.0297 AC: 1235 AN: 41540

American (AMR) AF: 0.139 AC: 2132 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.167 AC: 580 AN: 3468

East Asian (EAS) AF: 0.110 AC: 568 AN: 5182

South Asian (SAS) AF: 0.207 AC: 999 AN: 4824

European-Finnish (FIN) AF: 0.114 AC: 1213 AN: 10594

Middle Eastern (MID) AF: 0.143 AC: 42 AN: 294

European-Non Finnish (NFE) AF: 0.125 AC: 8483 AN: 67992

Other (OTH) AF: 0.115 AC: 242 AN: 2110

Alfa AF: 0.111 Hom.: 505

Bravo AF: 0.100

Asia WGS AF: 0.141 AC: 488 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.3
DANN	Benign	0.48
PhyloP100		1.3

Splicing

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

Other links and lift over

dbSNP: rs4128208; hg19: chr18-48794820;