rs12449964

Variant names:

• chr17-17641390-C-T
• rs12449964

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 0.358 in 151,622 control chromosomes in the GnomAD database, including 10,467 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 0.36 (10467 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.811

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.446 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: 0.359 AC: 54328 AN: 151512 Hom.: 10472 Cov.: 30

Gnomad AFR AF: 0.250

Gnomad AMI AF: 0.404

Gnomad AMR AF: 0.370

Gnomad ASJ AF: 0.431

Gnomad EAS AF: 0.122

Gnomad SAS AF: 0.207

Gnomad FIN AF: 0.331

Gnomad MID AF: 0.421

Gnomad NFE AF: 0.450

Gnomad OTH AF: 0.356

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

GnomAD4 genome AF: 0.358 AC: 54345 AN: 151622 Hom.: 10467 Cov.: 30 AF XY: 0.350 AC XY: 25897 AN XY: 74024

Gnomad4 AFR AF: 0.250

Gnomad4 AMR AF: 0.370

Gnomad4 ASJ AF: 0.431

Gnomad4 EAS AF: 0.122

Gnomad4 SAS AF: 0.206

Gnomad4 FIN AF: 0.331

Gnomad4 NFE AF: 0.450

Gnomad4 OTH AF: 0.353

Alfa AF: 0.431 Hom.: 24815

Bravo AF: 0.358

Asia WGS AF: 0.189 AC: 656 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.70
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: rs12449964; hg19: chr17-17544704;