rs1553441

Variant names:

• chr1-242546741-A-T
• rs1553441

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 0.239 in 152,152 control chromosomes in the GnomAD database, including 4,400 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 0.24 (4400 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.610

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.271 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: 0.239 AC: 36404 AN: 152034 Hom.: 4396 Cov.: 32

Gnomad AFR AF: 0.251

Gnomad AMI AF: 0.148

Gnomad AMR AF: 0.278

Gnomad ASJ AF: 0.190

Gnomad EAS AF: 0.272

Gnomad SAS AF: 0.174

Gnomad FIN AF: 0.234

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.231

Gnomad OTH AF: 0.250

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

GnomAD4 genome AF: 0.239 AC: 36431 AN: 152152 Hom.: 4400 Cov.: 32 AF XY: 0.239 AC XY: 17769 AN XY: 74388

Gnomad4 AFR AF: 0.251

Gnomad4 AMR AF: 0.278

Gnomad4 ASJ AF: 0.190

Gnomad4 EAS AF: 0.271

Gnomad4 SAS AF: 0.174

Gnomad4 FIN AF: 0.234

Gnomad4 NFE AF: 0.231

Gnomad4 OTH AF: 0.255

Alfa AF: 0.233 Hom.: 518

Bravo AF: 0.249

Asia WGS AF: 0.220 AC: 762 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	5.3
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1553441; hg19: chr1-242710043; COSMIC: COSV51783497;