rs4844553

Variant names:

• chr1-206761018-C-T
• rs4844553

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 0.0608 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
• Publications: 19 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.0734 AC: 3046 AN: 41510

American (AMR) AF: 0.0520 AC: 796 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0827 AC: 287 AN: 3470

East Asian (EAS) AF: 0.000964 AC: 5 AN: 5186

South Asian (SAS) AF: 0.0156 AC: 75 AN: 4818

European-Finnish (FIN) AF: 0.0629 AC: 667 AN: 10600

Middle Eastern (MID) AF: 0.0850 AC: 25 AN: 294

European-Non Finnish (NFE) AF: 0.0613 AC: 4171 AN: 68008

Other (OTH) AF: 0.0678 AC: 143 AN: 2108

Alfa AF: 0.0604 Hom.: 204

Bravo AF: 0.0623

Asia WGS AF: 0.0120 AC: 40 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.11
DANN	Benign	0.64
PhyloP100		-0.91

Splicing

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

Other links and lift over

dbSNP: rs4844553; hg19: chr1-206934363;