rs12900333

Variant names:

• chr15-78385934-C-T
• rs12900333
• ENST00000760515.1:n.77-5327C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000760515.1(ENSG00000299108):​n.77-5327C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0838 in 152,182 control chromosomes in the GnomAD database, including 643 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 0.084 (643 hom., cov: 32)
• Consequence: ENSG00000299108 ENST00000760515.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.327
• Publications: 3 publications found

Genes affected

ENSG00000299108 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.11 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
ENSG00000299108	ENST00000760515.1	n.77-5327C>T		intron_variant	Intron 1 of 2
ENSG00000299108	ENST00000760516.1	n.85-5327C>T		intron_variant	Intron 1 of 4
ENSG00000299108	ENST00000760517.1	n.70-5327C>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.0838 AC: 12748 AN: 152064 Hom.: 644 Cov.: 32

Gnomad AFR AF: 0.0504

Gnomad AMI AF: 0.0132

Gnomad AMR AF: 0.0758

Gnomad ASJ AF: 0.0986

Gnomad EAS AF: 0.0874

Gnomad SAS AF: 0.0504

Gnomad FIN AF: 0.0587

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.112

Gnomad OTH AF: 0.0794

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

GnomAD4 genome AF: 0.0838 AC: 12754 AN: 152182 Hom.: 643 Cov.: 32 AF XY: 0.0800 AC XY: 5949 AN XY: 74386

African (AFR) AF: 0.0504 AC: 2092 AN: 41516

American (AMR) AF: 0.0756 AC: 1156 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0986 AC: 342 AN: 3470

East Asian (EAS) AF: 0.0872 AC: 451 AN: 5174

South Asian (SAS) AF: 0.0513 AC: 247 AN: 4818

European-Finnish (FIN) AF: 0.0587 AC: 622 AN: 10590

Middle Eastern (MID) AF: 0.0850 AC: 25 AN: 294

European-Non Finnish (NFE) AF: 0.112 AC: 7640 AN: 68006

Other (OTH) AF: 0.0791 AC: 167 AN: 2112

Alfa AF: 0.104 Hom.: 2466

Bravo AF: 0.0850

Asia WGS AF: 0.0540 AC: 187 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.26
DANN	Benign	0.63
PhyloP100		-0.33

Splicing

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

Other links and lift over

dbSNP: rs12900333; hg19: chr15-78678276;