rs1553923

Variant names:

• chr4-30482533-A-C
• rs1553923

Your query was ambiguous. Multiple possible variants found:

• chr4-30482533-A-C
• chr4-30482533-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 0.177 in 152,094 control chromosomes in the GnomAD database, including 2,732 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 0.18 (2732 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.929
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.267 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: 0.177 AC: 26949 AN: 151978 Hom.: 2730 Cov.: 32

Gnomad AFR AF: 0.0927

Gnomad AMI AF: 0.136

Gnomad AMR AF: 0.192

Gnomad ASJ AF: 0.256

Gnomad EAS AF: 0.221

Gnomad SAS AF: 0.281

Gnomad FIN AF: 0.225

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.204

Gnomad OTH AF: 0.162

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

GnomAD4 genome AF: 0.177 AC: 26960 AN: 152094 Hom.: 2732 Cov.: 32 AF XY: 0.180 AC XY: 13395 AN XY: 74352

African (AFR) AF: 0.0929 AC: 3857 AN: 41524

American (AMR) AF: 0.192 AC: 2922 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.256 AC: 890 AN: 3470

East Asian (EAS) AF: 0.222 AC: 1146 AN: 5168

South Asian (SAS) AF: 0.280 AC: 1348 AN: 4820

European-Finnish (FIN) AF: 0.225 AC: 2383 AN: 10568

Middle Eastern (MID) AF: 0.180 AC: 53 AN: 294

European-Non Finnish (NFE) AF: 0.204 AC: 13896 AN: 67972

Other (OTH) AF: 0.161 AC: 341 AN: 2112

Alfa AF: 0.192 Hom.: 11509

Bravo AF: 0.168

Asia WGS AF: 0.269 AC: 936 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	7.0
DANN	Benign	0.46
PhyloP100		0.93

Splicing

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

Other links and lift over

dbSNP: rs1553923; hg19: chr4-30484155;