rs1288334

Variant names:

• chr1-53164999-T-C
• rs1288334

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 0.108 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.108 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

Gnomad4 AFR AF: 0.129

Gnomad4 AMR AF: 0.0845

Gnomad4 ASJ AF: 0.146

Gnomad4 EAS AF: 0.0721

Gnomad4 SAS AF: 0.0865

Gnomad4 FIN AF: 0.0940

Gnomad4 NFE AF: 0.104

Gnomad4 OTH AF: 0.109

Alfa AF: 0.104 Hom.: 102

Bravo AF: 0.109

Asia WGS AF: 0.0590 AC: 205 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	5.8
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1288334; hg19: chr1-53630671;