rs4128466

Variant names:

• chr4-135810619-G-C
• rs4128466

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 0.195 in 151,996 control chromosomes in the GnomAD database, including 3,110 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 0.19 (3110 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.04
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.301 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: 0.195 AC: 29569 AN: 151874 Hom.: 3105 Cov.: 32

Gnomad AFR AF: 0.166

Gnomad AMI AF: 0.148

Gnomad AMR AF: 0.280

Gnomad ASJ AF: 0.191

Gnomad EAS AF: 0.314

Gnomad SAS AF: 0.199

Gnomad FIN AF: 0.239

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.178

Gnomad OTH AF: 0.193

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

GnomAD4 genome AF: 0.195 AC: 29599 AN: 151996 Hom.: 3110 Cov.: 32 AF XY: 0.201 AC XY: 14927 AN XY: 74294

African (AFR) AF: 0.166 AC: 6865 AN: 41466

American (AMR) AF: 0.281 AC: 4284 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.191 AC: 662 AN: 3466

East Asian (EAS) AF: 0.313 AC: 1613 AN: 5148

South Asian (SAS) AF: 0.199 AC: 960 AN: 4816

European-Finnish (FIN) AF: 0.239 AC: 2523 AN: 10568

Middle Eastern (MID) AF: 0.137 AC: 40 AN: 292

European-Non Finnish (NFE) AF: 0.178 AC: 12108 AN: 67960

Other (OTH) AF: 0.194 AC: 409 AN: 2110

Alfa AF: 0.198 Hom.: 395

Bravo AF: 0.199

Asia WGS AF: 0.292 AC: 1015 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	0.31
DANN	Benign	0.50
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs4128466; hg19: chr4-136731774;