1-55034533-T-C

Variant names:

• chr1-55034533-T-C
• rs2495488

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 0.89 in 152,290 control chromosomes in the GnomAD database, including 60,592 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 0.89 (60592 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.393
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.941 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.891 AC: 135518 AN: 152172 Hom.: 60560 Cov.: 34

Gnomad AFR AF: 0.806

Gnomad AMI AF: 0.946

Gnomad AMR AF: 0.878

Gnomad ASJ AF: 0.934

Gnomad EAS AF: 0.927

Gnomad SAS AF: 0.963

Gnomad FIN AF: 0.914

Gnomad MID AF: 0.927

Gnomad NFE AF: 0.929

Gnomad OTH AF: 0.913

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

GnomAD4 genome AF: 0.890 AC: 135605 AN: 152290 Hom.: 60592 Cov.: 34 AF XY: 0.891 AC XY: 66379 AN XY: 74490

African (AFR) AF: 0.806 AC: 33461 AN: 41526

American (AMR) AF: 0.877 AC: 13423 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.934 AC: 3242 AN: 3470

East Asian (EAS) AF: 0.928 AC: 4809 AN: 5184

South Asian (SAS) AF: 0.964 AC: 4657 AN: 4830

European-Finnish (FIN) AF: 0.914 AC: 9710 AN: 10620

Middle Eastern (MID) AF: 0.929 AC: 273 AN: 294

European-Non Finnish (NFE) AF: 0.929 AC: 63236 AN: 68040

Other (OTH) AF: 0.913 AC: 1931 AN: 2114

Alfa AF: 0.916 Hom.: 109436

Bravo AF: 0.882

Asia WGS AF: 0.939 AC: 3265 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.9
DANN	Benign	0.51
PhyloP100		-0.39

Splicing

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

Other links and lift over

dbSNP: rs2495488; hg19: chr1-55500206;