rs1154433

Variant names:

• chr4-99332551-A-G
• rs1154433

Your query was ambiguous. Multiple possible variants found:

• chr4-99332551-A-G
• chr4-99332551-A-T

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 0.314 in 151,954 control chromosomes in the GnomAD database, including 8,902 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 0.31 (8902 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.42
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.409 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: 0.314 AC: 47645 AN: 151834 Hom.: 8895 Cov.: 32

Gnomad AFR AF: 0.145

Gnomad AMI AF: 0.230

Gnomad AMR AF: 0.295

Gnomad ASJ AF: 0.274

Gnomad EAS AF: 0.0818

Gnomad SAS AF: 0.297

Gnomad FIN AF: 0.513

Gnomad MID AF: 0.255

Gnomad NFE AF: 0.413

Gnomad OTH AF: 0.284

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

GnomAD4 genome AF: 0.314 AC: 47666 AN: 151954 Hom.: 8902 Cov.: 32 AF XY: 0.314 AC XY: 23352 AN XY: 74260

African (AFR) AF: 0.145 AC: 6021 AN: 41478

American (AMR) AF: 0.295 AC: 4504 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.274 AC: 949 AN: 3466

East Asian (EAS) AF: 0.0814 AC: 421 AN: 5172

South Asian (SAS) AF: 0.298 AC: 1437 AN: 4822

European-Finnish (FIN) AF: 0.513 AC: 5411 AN: 10538

Middle Eastern (MID) AF: 0.243 AC: 71 AN: 292

European-Non Finnish (NFE) AF: 0.413 AC: 28037 AN: 67914

Other (OTH) AF: 0.287 AC: 606 AN: 2112

Alfa AF: 0.265 Hom.: 859

Bravo AF: 0.288

Asia WGS AF: 0.221 AC: 766 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.39
DANN	Benign	0.41
PhyloP100		-3.4

Splicing

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

Other links and lift over

dbSNP: rs1154433; hg19: chr4-100253708;