rs8027941

Variant names:

• chr15-92358910-C-T
• rs8027941
• ENST00000838102.1:n.775+1574G>A

Variant summary

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

The ENST00000838102.1(ENSG00000309057):​n.775+1574G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.216 in 151,952 control chromosomes in the GnomAD database, including 4,883 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 0.22 (4883 hom., cov: 32)
• Consequence: ENSG00000309057 ENST00000838102.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.10
• Publications: 1 publications found

Genes affected

ENSG00000309057 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.419 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
ENSG00000309057	ENST00000838102.1	n.775+1574G>A		intron_variant	Intron 5 of 9
ENSG00000309057	ENST00000838104.1	n.512+1574G>A		intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes AF: 0.216 AC: 32723 AN: 151834 Hom.: 4870 Cov.: 32

Gnomad AFR AF: 0.424

Gnomad AMI AF: 0.184

Gnomad AMR AF: 0.133

Gnomad ASJ AF: 0.185

Gnomad EAS AF: 0.0135

Gnomad SAS AF: 0.0726

Gnomad FIN AF: 0.121

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.150

Gnomad OTH AF: 0.204

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

GnomAD4 genome AF: 0.216 AC: 32770 AN: 151952 Hom.: 4883 Cov.: 32 AF XY: 0.207 AC XY: 15364 AN XY: 74266

African (AFR) AF: 0.424 AC: 17558 AN: 41412

American (AMR) AF: 0.133 AC: 2026 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.185 AC: 643 AN: 3472

East Asian (EAS) AF: 0.0135 AC: 70 AN: 5178

South Asian (SAS) AF: 0.0719 AC: 346 AN: 4814

European-Finnish (FIN) AF: 0.121 AC: 1272 AN: 10516

Middle Eastern (MID) AF: 0.173 AC: 51 AN: 294

European-Non Finnish (NFE) AF: 0.150 AC: 10209 AN: 67978

Other (OTH) AF: 0.202 AC: 428 AN: 2114

Alfa AF: 0.192 Hom.: 502

Bravo AF: 0.227

Asia WGS AF: 0.0750 AC: 261 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	6.9
DANN	Benign	0.61
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs8027941; hg19: chr15-92902140;