15-92380717-G-C

Variant names:

• chr15-92380717-G-C
• rs56027313
• ENST00000838102.1:n.379-7853C>G

Variant summary

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

The ENST00000838102.1(ENSG00000309057):​n.379-7853C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.709 in 145,864 control chromosomes in the GnomAD database, including 38,428 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 0.71 (38428 hom., cov: 26)
• Consequence: ENSG00000309057 ENST00000838102.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.679
• Publications: 4 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=-1.06).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.843 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.379-7853C>G		intron_variant	Intron 1 of 9
ENSG00000309057	ENST00000838103.1	n.412-7853C>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.709 AC: 103370 AN: 145754 Hom.: 38435 Cov.: 26

Gnomad AFR AF: 0.479

Gnomad AMI AF: 0.927

Gnomad AMR AF: 0.635

Gnomad ASJ AF: 0.810

Gnomad EAS AF: 0.421

Gnomad SAS AF: 0.680

Gnomad FIN AF: 0.850

Gnomad MID AF: 0.728

Gnomad NFE AF: 0.849

Gnomad OTH AF: 0.687

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

GnomAD4 genome AF: 0.709 AC: 103375 AN: 145864 Hom.: 38428 Cov.: 26 AF XY: 0.704 AC XY: 49990 AN XY: 70972

African (AFR) AF: 0.478 AC: 18074 AN: 37812

American (AMR) AF: 0.634 AC: 9199 AN: 14516

Ashkenazi Jewish (ASJ) AF: 0.810 AC: 2784 AN: 3438

East Asian (EAS) AF: 0.422 AC: 2073 AN: 4912

South Asian (SAS) AF: 0.680 AC: 3035 AN: 4466

European-Finnish (FIN) AF: 0.850 AC: 8612 AN: 10126

Middle Eastern (MID) AF: 0.716 AC: 209 AN: 292

European-Non Finnish (NFE) AF: 0.849 AC: 57159 AN: 67364

Other (OTH) AF: 0.685 AC: 1394 AN: 2036

Alfa AF: 0.759 Hom.: 4733

Asia WGS AF: 0.481 AC: 1612 AN: 3344

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	1.2
DANN	Benign	0.28
PhyloP100		-0.68

Splicing

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

Other links and lift over

dbSNP: rs56027313; hg19: chr15-92923947;