15-33227964-T-G

Variant names:

• chr15-33227964-T-G
• rs12908716

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 0.591 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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.708 AC: 29341 AN: 41444

American (AMR) AF: 0.511 AC: 7806 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.540 AC: 1875 AN: 3470

East Asian (EAS) AF: 0.721 AC: 3729 AN: 5172

South Asian (SAS) AF: 0.593 AC: 2860 AN: 4822

European-Finnish (FIN) AF: 0.509 AC: 5378 AN: 10560

Middle Eastern (MID) AF: 0.613 AC: 179 AN: 292

European-Non Finnish (NFE) AF: 0.544 AC: 36990 AN: 67952

Other (OTH) AF: 0.566 AC: 1197 AN: 2116

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
PhyloP100		-0.82

Splicing

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

Other links and lift over

dbSNP: rs12908716; hg19: chr15-33520165;