rs8033165

Variant names:

• chr15-28760947-C-T
• rs8033165
• ENST00000796254.1:n.1539-2928C>T

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000796254.1(ENSG00000290879):​n.1539-2928C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.313 in 150,274 control chromosomes in the GnomAD database, including 8,695 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 0.31 (8695 hom., cov: 28)
• Consequence: ENSG00000290879 ENST00000796254.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.23
• Publications: 20 publications found

Genes affected

ENSG00000290879 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.35).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.436 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
ENSG00000290879	ENST00000796254.1	n.1539-2928C>T		intron_variant	Intron 9 of 9
ENSG00000290879	ENST00000796261.1	n.1509+14C>T		intron_variant	Intron 11 of 11
ENSG00000290879	ENST00000796263.1	n.1177+14C>T		intron_variant	Intron 9 of 9

Frequencies

GnomAD3 genomes AF: 0.313 AC: 46962 AN: 150158 Hom.: 8694 Cov.: 28

Gnomad AFR AF: 0.164

Gnomad AMI AF: 0.454

Gnomad AMR AF: 0.193

Gnomad ASJ AF: 0.266

Gnomad EAS AF: 0.00118

Gnomad SAS AF: 0.122

Gnomad FIN AF: 0.496

Gnomad MID AF: 0.222

Gnomad NFE AF: 0.440

Gnomad OTH AF: 0.270

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

GnomAD4 genome AF: 0.313 AC: 46966 AN: 150274 Hom.: 8695 Cov.: 28 AF XY: 0.306 AC XY: 22464 AN XY: 73330

African (AFR) AF: 0.164 AC: 6689 AN: 40778

American (AMR) AF: 0.193 AC: 2914 AN: 15112

Ashkenazi Jewish (ASJ) AF: 0.266 AC: 917 AN: 3452

East Asian (EAS) AF: 0.00118 AC: 6 AN: 5084

South Asian (SAS) AF: 0.123 AC: 586 AN: 4776

European-Finnish (FIN) AF: 0.496 AC: 5110 AN: 10300

Middle Eastern (MID) AF: 0.221 AC: 65 AN: 294

European-Non Finnish (NFE) AF: 0.440 AC: 29712 AN: 67500

Other (OTH) AF: 0.269 AC: 562 AN: 2086

Alfa AF: 0.361 Hom.: 7564

Bravo AF: 0.287

Asia WGS AF: 0.100 AC: 351 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.35
CADD	Benign	23
DANN	Benign	0.87
PhyloP100		2.2

Splicing

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

Other links and lift over

dbSNP: rs8033165; hg19: chr15-29006093;