rs12449964

Positions:

• chr17-17641390-C-T

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;