rs1408229

Variant names:

• chr13-37230216-A-C
• rs1408229

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;