rs1332498

chr1-152717972-T-C

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 0.381 in 151,770 control chromosomes in the GnomAD database, including 11,581 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 0.38 (11581 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.800

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.494 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.381 AC: 57738 AN: 151650 Hom.: 11562 Cov.: 31

Gnomad AFR AF: 0.499

Gnomad AMI AF: 0.286

Gnomad AMR AF: 0.374

Gnomad ASJ AF: 0.270

Gnomad EAS AF: 0.163

Gnomad SAS AF: 0.225

Gnomad FIN AF: 0.305

Gnomad MID AF: 0.347

Gnomad NFE AF: 0.357

Gnomad OTH AF: 0.372

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

GnomAD4 genome AF: 0.381 AC: 57794 AN: 151770 Hom.: 11581 Cov.: 31 AF XY: 0.375 AC XY: 27797 AN XY: 74178

Gnomad4 AFR AF: 0.499

Gnomad4 AMR AF: 0.374

Gnomad4 ASJ AF: 0.270

Gnomad4 EAS AF: 0.164

Gnomad4 SAS AF: 0.225

Gnomad4 FIN AF: 0.305

Gnomad4 NFE AF: 0.357

Gnomad4 OTH AF: 0.368

Alfa AF: 0.351 Hom.: 11346

Bravo AF: 0.389

Asia WGS AF: 0.211 AC: 735 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	1.1
Dann	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1332498; hg19: chr1-152690448;