15-33227964-T-G

Variant names:

• chr15-33227964-T-G
• rs12908716

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 0.591 in 152,022 control chromosomes in the GnomAD database, including 27,109 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 0.59 (27109 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.818

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 = 0.702 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: 0.591 AC: 89823 AN: 151904 Hom.: 27083 Cov.: 33

Gnomad AFR AF: 0.708

Gnomad AMI AF: 0.593

Gnomad AMR AF: 0.511

Gnomad ASJ AF: 0.540

Gnomad EAS AF: 0.722

Gnomad SAS AF: 0.593

Gnomad FIN AF: 0.509

Gnomad MID AF: 0.602

Gnomad NFE AF: 0.544

Gnomad OTH AF: 0.567

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

GnomAD4 genome AF: 0.591 AC: 89895 AN: 152022 Hom.: 27109 Cov.: 33 AF XY: 0.588 AC XY: 43664 AN XY: 74316

Gnomad4 AFR AF: 0.708

Gnomad4 AMR AF: 0.511

Gnomad4 ASJ AF: 0.540

Gnomad4 EAS AF: 0.721

Gnomad4 SAS AF: 0.593

Gnomad4 FIN AF: 0.509

Gnomad4 NFE AF: 0.544

Gnomad4 OTH AF: 0.566

Alfa AF: 0.561 Hom.: 4914

Bravo AF: 0.594

Asia WGS AF: 0.622 AC: 2163 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	0.23
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12908716; hg19: chr15-33520165;