rs3024523

Positions:

• chr1-206869339-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 0.0554 in 152,288 control chromosomes in the GnomAD database, including 422 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 0.055 (422 hom., cov: 32)
  • Exomes 𝑓: 0.013 (0 hom.)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.632

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 = 0.125 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: 0.0553 AC: 8403 AN: 152014 Hom.: 415 Cov.: 32

Gnomad AFR AF: 0.127

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0353

Gnomad ASJ AF: 0.0259

Gnomad EAS AF: 0.0381

Gnomad SAS AF: 0.0348

Gnomad FIN AF: 0.0267

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0257

Gnomad OTH AF: 0.0503

GnomAD4 exome AF: 0.0128 AC: 2 AN: 156 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 94

Gnomad4 EAS exome AF: 0.0149

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.0555 AC: 8438 AN: 152132 Hom.: 422 Cov.: 32 AF XY: 0.0539 AC XY: 4013 AN XY: 74394

Gnomad4 AFR AF: 0.128

Gnomad4 AMR AF: 0.0353

Gnomad4 ASJ AF: 0.0259

Gnomad4 EAS AF: 0.0382

Gnomad4 SAS AF: 0.0349

Gnomad4 FIN AF: 0.0267

Gnomad4 NFE AF: 0.0256

Gnomad4 OTH AF: 0.0498

Alfa AF: 0.0587 Hom.: 72

Bravo AF: 0.0618

Asia WGS AF: 0.0430 AC: 149 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	1.8
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3024523; hg19: chr1-207042684;