rs4844553

Variant names:

• chr1-206761018-C-T
• rs4844553

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 0.0608 in 152,200 control chromosomes in the GnomAD database, including 284 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 0.061 (284 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.910

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0712 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: 0.0608 AC: 9250 AN: 152082 Hom.: 284 Cov.: 31

Gnomad AFR AF: 0.0735

Gnomad AMI AF: 0.0406

Gnomad AMR AF: 0.0521

Gnomad ASJ AF: 0.0827

Gnomad EAS AF: 0.000962

Gnomad SAS AF: 0.0156

Gnomad FIN AF: 0.0629

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.0613

Gnomad OTH AF: 0.0686

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

GnomAD4 genome AF: 0.0608 AC: 9252 AN: 152200 Hom.: 284 Cov.: 31 AF XY: 0.0603 AC XY: 4484 AN XY: 74412

Gnomad4 AFR AF: 0.0734

Gnomad4 AMR AF: 0.0520

Gnomad4 ASJ AF: 0.0827

Gnomad4 EAS AF: 0.000964

Gnomad4 SAS AF: 0.0156

Gnomad4 FIN AF: 0.0629

Gnomad4 NFE AF: 0.0613

Gnomad4 OTH AF: 0.0678

Alfa AF: 0.0605 Hom.: 188

Bravo AF: 0.0623

Asia WGS AF: 0.0120 AC: 40 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.11
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4844553; hg19: chr1-206934363;