rs6487465

Positions:

• chr12-25257349-T-C
• chr12-25257349-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 0.316 in 152,002 control chromosomes in the GnomAD database, including 7,794 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 0.32 (7794 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.481

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.408 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.316 AC: 48059 AN: 151884 Hom.: 7776 Cov.: 32

Gnomad AFR AF: 0.264

Gnomad AMI AF: 0.257

Gnomad AMR AF: 0.350

Gnomad ASJ AF: 0.389

Gnomad EAS AF: 0.422

Gnomad SAS AF: 0.273

Gnomad FIN AF: 0.295

Gnomad MID AF: 0.326

Gnomad NFE AF: 0.336

Gnomad OTH AF: 0.319

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

GnomAD4 genome AF: 0.316 AC: 48106 AN: 152002 Hom.: 7794 Cov.: 32 AF XY: 0.316 AC XY: 23514 AN XY: 74304

Gnomad4 AFR AF: 0.264

Gnomad4 AMR AF: 0.350

Gnomad4 ASJ AF: 0.389

Gnomad4 EAS AF: 0.423

Gnomad4 SAS AF: 0.275

Gnomad4 FIN AF: 0.295

Gnomad4 NFE AF: 0.336

Gnomad4 OTH AF: 0.321

Alfa AF: 0.334 Hom.: 17785

Bravo AF: 0.322

Asia WGS AF: 0.348 AC: 1212 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	3.6
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6487465; hg19: chr12-25410283;