15-92379618-A-T

Variant names:

• chr15-92379618-A-T
• rs10852173
• ENST00000838102.1:n.379-6754T>A

Variant summary

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

The ENST00000838102.1(ENSG00000309057):​n.379-6754T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.683 in 152,162 control chromosomes in the GnomAD database, including 37,982 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 0.68 (37982 hom., cov: 33)
• Consequence: ENSG00000309057 ENST00000838102.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.685
• Publications: 5 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=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.83 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.379-6754T>A		intron_variant	Intron 1 of 9
ENSG00000309057	ENST00000838103.1	n.412-6754T>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.684 AC: 103986 AN: 152044 Hom.: 37989 Cov.: 33

Gnomad AFR AF: 0.449

Gnomad AMI AF: 0.924

Gnomad AMR AF: 0.606

Gnomad ASJ AF: 0.806

Gnomad EAS AF: 0.410

Gnomad SAS AF: 0.655

Gnomad FIN AF: 0.824

Gnomad MID AF: 0.722

Gnomad NFE AF: 0.836

Gnomad OTH AF: 0.667

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

GnomAD4 genome AF: 0.683 AC: 103992 AN: 152162 Hom.: 37982 Cov.: 33 AF XY: 0.678 AC XY: 50448 AN XY: 74394

African (AFR) AF: 0.448 AC: 18601 AN: 41480

American (AMR) AF: 0.605 AC: 9260 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.806 AC: 2797 AN: 3472

East Asian (EAS) AF: 0.410 AC: 2122 AN: 5172

South Asian (SAS) AF: 0.655 AC: 3157 AN: 4822

European-Finnish (FIN) AF: 0.824 AC: 8733 AN: 10592

Middle Eastern (MID) AF: 0.711 AC: 209 AN: 294

European-Non Finnish (NFE) AF: 0.836 AC: 56866 AN: 68004

Other (OTH) AF: 0.665 AC: 1404 AN: 2112

Alfa AF: 0.722 Hom.: 2800

Bravo AF: 0.654

Asia WGS AF: 0.507 AC: 1767 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	6.8
DANN	Benign	0.76
PhyloP100		0.69

Splicing

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

Other links and lift over

dbSNP: rs10852173; hg19: chr15-92922848;