rs1553432

Variant names:

• chr4-99502293-A-G
• rs1553432

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 0.0485 in 152,268 control chromosomes in the GnomAD database, including 311 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 0.048 (311 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.849
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0641 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: 0.0485 AC: 7385 AN: 152150 Hom.: 311 Cov.: 32

Gnomad AFR AF: 0.0117

Gnomad AMI AF: 0.159

Gnomad AMR AF: 0.0557

Gnomad ASJ AF: 0.188

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.0296

Gnomad FIN AF: 0.0421

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.0657

Gnomad OTH AF: 0.0746

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

GnomAD4 genome AF: 0.0485 AC: 7384 AN: 152268 Hom.: 311 Cov.: 32 AF XY: 0.0484 AC XY: 3604 AN XY: 74438

African (AFR) AF: 0.0117 AC: 486 AN: 41570

American (AMR) AF: 0.0556 AC: 849 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.188 AC: 652 AN: 3472

East Asian (EAS) AF: 0.000386 AC: 2 AN: 5188

South Asian (SAS) AF: 0.0298 AC: 144 AN: 4828

European-Finnish (FIN) AF: 0.0421 AC: 446 AN: 10602

Middle Eastern (MID) AF: 0.129 AC: 38 AN: 294

European-Non Finnish (NFE) AF: 0.0657 AC: 4466 AN: 68010

Other (OTH) AF: 0.0739 AC: 156 AN: 2112

Alfa AF: 0.0476 Hom.: 71

Bravo AF: 0.0486

Asia WGS AF: 0.0170 AC: 59 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	3.3
DANN	Benign	0.83
PhyloP100		0.85

Splicing

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

Other links and lift over

dbSNP: rs1553432; hg19: chr4-100423450;