1-55035303-C-T

Variant names:

• chr1-55035303-C-T
• rs10788994

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 0.21 in 152,194 control chromosomes in the GnomAD database, including 4,104 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 0.21 (4104 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0860
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.633 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: 0.209 AC: 31858 AN: 152076 Hom.: 4090 Cov.: 33

Gnomad AFR AF: 0.185

Gnomad AMI AF: 0.189

Gnomad AMR AF: 0.284

Gnomad ASJ AF: 0.255

Gnomad EAS AF: 0.651

Gnomad SAS AF: 0.211

Gnomad FIN AF: 0.110

Gnomad MID AF: 0.266

Gnomad NFE AF: 0.186

Gnomad OTH AF: 0.236

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

GnomAD4 genome AF: 0.210 AC: 31914 AN: 152194 Hom.: 4104 Cov.: 33 AF XY: 0.210 AC XY: 15647 AN XY: 74420

African (AFR) AF: 0.185 AC: 7700 AN: 41522

American (AMR) AF: 0.285 AC: 4352 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.255 AC: 886 AN: 3472

East Asian (EAS) AF: 0.651 AC: 3370 AN: 5174

South Asian (SAS) AF: 0.212 AC: 1022 AN: 4828

European-Finnish (FIN) AF: 0.110 AC: 1164 AN: 10592

Middle Eastern (MID) AF: 0.262 AC: 77 AN: 294

European-Non Finnish (NFE) AF: 0.186 AC: 12664 AN: 67998

Other (OTH) AF: 0.240 AC: 507 AN: 2112

Alfa AF: 0.197 Hom.: 1119

Bravo AF: 0.225

Asia WGS AF: 0.409 AC: 1419 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	6.6
DANN	Benign	0.73
PhyloP100		0.086

Splicing

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

Other links and lift over

dbSNP: rs10788994; hg19: chr1-55500976;