rs12407665

Variant names:

• chr1-13871220-T-C
• rs12407665

Your query was ambiguous. Multiple possible variants found:

• chr1-13871220-T-C
• chr1-13871220-T-G

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 0.349 in 152,084 control chromosomes in the GnomAD database, including 10,294 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 0.35 (10294 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0510

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.703 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: 0.349 AC: 53059 AN: 151964 Hom.: 10274 Cov.: 32

Gnomad AFR AF: 0.235

Gnomad AMI AF: 0.356

Gnomad AMR AF: 0.478

Gnomad ASJ AF: 0.280

Gnomad EAS AF: 0.722

Gnomad SAS AF: 0.441

Gnomad FIN AF: 0.451

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.343

Gnomad OTH AF: 0.353

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

GnomAD4 genome AF: 0.349 AC: 53123 AN: 152084 Hom.: 10294 Cov.: 32 AF XY: 0.359 AC XY: 26703 AN XY: 74326

Gnomad4 AFR AF: 0.235

Gnomad4 AMR AF: 0.479

Gnomad4 ASJ AF: 0.280

Gnomad4 EAS AF: 0.722

Gnomad4 SAS AF: 0.441

Gnomad4 FIN AF: 0.451

Gnomad4 NFE AF: 0.343

Gnomad4 OTH AF: 0.358

Alfa AF: 0.347 Hom.: 12398

Bravo AF: 0.350

Asia WGS AF: 0.570 AC: 1976 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	3.6
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12407665; hg19: chr1-14197715;