rs1408229

chr13-37230216-A-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 0.645 in 486,974 control chromosomes in the GnomAD database, including 103,679 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 0.64 (31792 hom., cov: 31)
  • Exomes 𝑓: 0.65 (71887 hom.)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.62

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.687 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: 0.642 AC: 97449 AN: 151816 Hom.: 31769 Cov.: 31

Gnomad AFR AF: 0.636

Gnomad AMI AF: 0.501

Gnomad AMR AF: 0.634

Gnomad ASJ AF: 0.689

Gnomad EAS AF: 0.224

Gnomad SAS AF: 0.575

Gnomad FIN AF: 0.584

Gnomad MID AF: 0.662

Gnomad NFE AF: 0.692

Gnomad OTH AF: 0.656

GnomAD3 exomes AF: 0.625 AC: 114267 AN: 182902 Hom.: 37240 AF XY: 0.624 AC XY: 62247 AN XY: 99716

Gnomad AFR exome AF: 0.635

Gnomad AMR exome AF: 0.656

Gnomad ASJ exome AF: 0.701

Gnomad EAS exome AF: 0.215

Gnomad SAS exome AF: 0.604

Gnomad FIN exome AF: 0.600

Gnomad NFE exome AF: 0.686

Gnomad OTH exome AF: 0.660

GnomAD4 exome AF: 0.647 AC: 216690 AN: 335040 Hom.: 71887 Cov.: 0 AF XY: 0.643 AC XY: 122839 AN XY: 191042

Gnomad4 AFR exome AF: 0.635

Gnomad4 AMR exome AF: 0.658

Gnomad4 ASJ exome AF: 0.702

Gnomad4 EAS exome AF: 0.214

Gnomad4 SAS exome AF: 0.600

Gnomad4 FIN exome AF: 0.606

Gnomad4 NFE exome AF: 0.692

Gnomad4 OTH exome AF: 0.648

GnomAD4 genome AF: 0.642 AC: 97508 AN: 151934 Hom.: 31792 Cov.: 31 AF XY: 0.634 AC XY: 47107 AN XY: 74266

Gnomad4 AFR AF: 0.635

Gnomad4 AMR AF: 0.635

Gnomad4 ASJ AF: 0.689

Gnomad4 EAS AF: 0.224

Gnomad4 SAS AF: 0.574

Gnomad4 FIN AF: 0.584

Gnomad4 NFE AF: 0.692

Gnomad4 OTH AF: 0.652

Alfa AF: 0.677 Hom.: 8020

Bravo AF: 0.645

Asia WGS AF: 0.425 AC: 1482 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	0.17
Dann	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1408229; hg19: chr13-37804353; COSMIC: COSV61339060;