rs6487465

Variant names:

• chr12-25257349-T-C
• rs6487465

Your query was ambiguous. Multiple possible variants found:

• chr12-25257349-T-C
• chr12-25257349-T-G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 10 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.264 AC: 10928 AN: 41426

American (AMR) AF: 0.350 AC: 5353 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.389 AC: 1349 AN: 3470

East Asian (EAS) AF: 0.423 AC: 2181 AN: 5162

South Asian (SAS) AF: 0.275 AC: 1325 AN: 4826

European-Finnish (FIN) AF: 0.295 AC: 3119 AN: 10560

Middle Eastern (MID) AF: 0.340 AC: 100 AN: 294

European-Non Finnish (NFE) AF: 0.336 AC: 22840 AN: 67968

Other (OTH) AF: 0.321 AC: 678 AN: 2112

Alfa AF: 0.334 Hom.: 38081

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
PhyloP100		0.48

Splicing

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

Other links and lift over

dbSNP: rs6487465; hg19: chr12-25410283;