rs12602832

chr17-44319528-C-T

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 0.0712 in 185,924 control chromosomes in the GnomAD database, including 655 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 0.072 (549 hom., cov: 32)
  • Exomes 𝑓: 0.067 (106 hom.)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.971

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.111 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: 0.0723 AC: 10999 AN: 152154 Hom.: 549 Cov.: 32

Gnomad AFR AF: 0.0192

Gnomad AMI AF: 0.0319

Gnomad AMR AF: 0.114

Gnomad ASJ AF: 0.0496

Gnomad EAS AF: 0.0330

Gnomad SAS AF: 0.119

Gnomad FIN AF: 0.128

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.0881

Gnomad OTH AF: 0.0817

GnomAD4 exome AF: 0.0667 AC: 2244 AN: 33652 Hom.: 106 AF XY: 0.0670 AC XY: 1182 AN XY: 17634

Gnomad4 AFR exome AF: 0.0142

Gnomad4 AMR exome AF: 0.0951

Gnomad4 ASJ exome AF: 0.0368

Gnomad4 EAS exome AF: 0.0304

Gnomad4 SAS exome AF: 0.0841

Gnomad4 FIN exome AF: 0.0883

Gnomad4 NFE exome AF: 0.0640

Gnomad4 OTH exome AF: 0.0616

GnomAD4 genome AF: 0.0722 AC: 10999 AN: 152272 Hom.: 549 Cov.: 32 AF XY: 0.0752 AC XY: 5596 AN XY: 74446

Gnomad4 AFR AF: 0.0191

Gnomad4 AMR AF: 0.114

Gnomad4 ASJ AF: 0.0496

Gnomad4 EAS AF: 0.0334

Gnomad4 SAS AF: 0.119

Gnomad4 FIN AF: 0.128

Gnomad4 NFE AF: 0.0881

Gnomad4 OTH AF: 0.0799

Alfa AF: 0.0777 Hom.: 501

Bravo AF: 0.0676

Asia WGS AF: 0.0800 AC: 280 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
Cadd	Benign	1.1
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: rs12602832; hg19: chr17-42396896;