rs950828

Variant names:

• chr4-133732297-T-A
• rs950828

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 0.203 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
• Publications: 3 publications found

ACMG classification

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

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.0586 AC: 2435 AN: 41558

American (AMR) AF: 0.294 AC: 4490 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.281 AC: 976 AN: 3470

East Asian (EAS) AF: 0.0319 AC: 165 AN: 5176

South Asian (SAS) AF: 0.251 AC: 1210 AN: 4826

European-Finnish (FIN) AF: 0.268 AC: 2839 AN: 10574

Middle Eastern (MID) AF: 0.279 AC: 82 AN: 294

European-Non Finnish (NFE) AF: 0.265 AC: 17989 AN: 67986

Other (OTH) AF: 0.228 AC: 482 AN: 2110

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
PhyloP100		0.34

Splicing

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

Other links and lift over

dbSNP: rs950828; hg19: chr4-134653452;