rs950828

chr4-133732297-T-A

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 0.203 in 152,188 control chromosomes in the GnomAD database, including 4,055 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 0.20 (4055 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.339

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.287 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.203 AC: 30909 AN: 152072 Hom.: 4054 Cov.: 32

Gnomad AFR AF: 0.0587

Gnomad AMI AF: 0.268

Gnomad AMR AF: 0.294

Gnomad ASJ AF: 0.281

Gnomad EAS AF: 0.0324

Gnomad SAS AF: 0.250

Gnomad FIN AF: 0.268

Gnomad MID AF: 0.288

Gnomad NFE AF: 0.265

Gnomad OTH AF: 0.229

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

GnomAD4 genome AF: 0.203 AC: 30912 AN: 152188 Hom.: 4055 Cov.: 32 AF XY: 0.205 AC XY: 15265 AN XY: 74390

Gnomad4 AFR AF: 0.0586

Gnomad4 AMR AF: 0.294

Gnomad4 ASJ AF: 0.281

Gnomad4 EAS AF: 0.0319

Gnomad4 SAS AF: 0.251

Gnomad4 FIN AF: 0.268

Gnomad4 NFE AF: 0.265

Gnomad4 OTH AF: 0.228

Alfa AF: 0.238 Hom.: 623

Bravo AF: 0.198

Asia WGS AF: 0.146 AC: 510 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	3.4
Dann	Benign	0.27

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs950828; hg19: chr4-134653452;