chr1-53164999-T-C

Variant names:

• chr1-53164999-T-C
• rs1288334

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 0.108 in 152,146 control chromosomes in the GnomAD database, including 893 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 0.11 (893 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.487
• Publications: 2 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 (AFR) allele frequency at 95% confidence interval = 0.126 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: 0.108 AC: 16344 AN: 152028 Hom.: 890 Cov.: 32

Gnomad AFR AF: 0.129

Gnomad AMI AF: 0.0855

Gnomad AMR AF: 0.0846

Gnomad ASJ AF: 0.146

Gnomad EAS AF: 0.0721

Gnomad SAS AF: 0.0860

Gnomad FIN AF: 0.0940

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.104

Gnomad OTH AF: 0.110

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

GnomAD4 genome AF: 0.108 AC: 16357 AN: 152146 Hom.: 893 Cov.: 32 AF XY: 0.105 AC XY: 7834 AN XY: 74394

African (AFR) AF: 0.129 AC: 5346 AN: 41490

American (AMR) AF: 0.0845 AC: 1291 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.146 AC: 505 AN: 3470

East Asian (EAS) AF: 0.0721 AC: 373 AN: 5176

South Asian (SAS) AF: 0.0865 AC: 417 AN: 4822

European-Finnish (FIN) AF: 0.0940 AC: 996 AN: 10594

Middle Eastern (MID) AF: 0.122 AC: 36 AN: 294

European-Non Finnish (NFE) AF: 0.104 AC: 7086 AN: 67998

Other (OTH) AF: 0.109 AC: 229 AN: 2104

Alfa AF: 0.106 Hom.: 112

Bravo AF: 0.109

Asia WGS AF: 0.0590 AC: 205 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	5.8
DANN	Benign	0.71
PhyloP100		0.49

Splicing

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

Other links and lift over

dbSNP: rs1288334; hg19: chr1-53630671;