rs1288331

Variant names:

• chr1-53165377-T-C
• rs1288331

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 0.366 in 152,070 control chromosomes in the GnomAD database, including 10,484 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 0.37 (10484 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.179

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.597 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: 0.366 AC: 55630 AN: 151952 Hom.: 10462 Cov.: 32

Gnomad AFR AF: 0.318

Gnomad AMI AF: 0.314

Gnomad AMR AF: 0.311

Gnomad ASJ AF: 0.353

Gnomad EAS AF: 0.362

Gnomad SAS AF: 0.614

Gnomad FIN AF: 0.368

Gnomad MID AF: 0.304

Gnomad NFE AF: 0.392

Gnomad OTH AF: 0.358

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

GnomAD4 genome AF: 0.366 AC: 55689 AN: 152070 Hom.: 10484 Cov.: 32 AF XY: 0.367 AC XY: 27278 AN XY: 74318

Gnomad4 AFR AF: 0.319

Gnomad4 AMR AF: 0.311

Gnomad4 ASJ AF: 0.353

Gnomad4 EAS AF: 0.362

Gnomad4 SAS AF: 0.615

Gnomad4 FIN AF: 0.368

Gnomad4 NFE AF: 0.392

Gnomad4 OTH AF: 0.356

Alfa AF: 0.392 Hom.: 15422

Bravo AF: 0.351

Asia WGS AF: 0.490 AC: 1699 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.4
DANN	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1288331; hg19: chr1-53631049;