15-92383521-T-G

Variant names:

• chr15-92383521-T-G
• rs13379489
• ENST00000838102.1:n.378+10543A>C

Variant summary

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

The ENST00000838102.1(ENSG00000309057):​n.378+10543A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.739 in 152,088 control chromosomes in the GnomAD database, including 42,920 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 0.74 (42920 hom., cov: 32)
• Consequence: ENSG00000309057 ENST00000838102.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.748
• Publications: 7 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=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.847 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000838102.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000309057	ENST00000838102.1		n.378+10543A>C		intron	N/A
	ENSG00000309057	ENST00000838103.1		n.411+8751A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.740 AC: 112410 AN: 151970 Hom.: 42923 Cov.: 32

Gnomad AFR AF: 0.602

Gnomad AMI AF: 0.924

Gnomad AMR AF: 0.645

Gnomad ASJ AF: 0.810

Gnomad EAS AF: 0.420

Gnomad SAS AF: 0.670

Gnomad FIN AF: 0.838

Gnomad MID AF: 0.753

Gnomad NFE AF: 0.853

Gnomad OTH AF: 0.727

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

GnomAD4 genome AF: 0.739 AC: 112423 AN: 152088 Hom.: 42920 Cov.: 32 AF XY: 0.733 AC XY: 54476 AN XY: 74334

African (AFR) AF: 0.601 AC: 24904 AN: 41434

American (AMR) AF: 0.644 AC: 9858 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.810 AC: 2814 AN: 3472

East Asian (EAS) AF: 0.421 AC: 2173 AN: 5164

South Asian (SAS) AF: 0.670 AC: 3222 AN: 4810

European-Finnish (FIN) AF: 0.838 AC: 8867 AN: 10582

Middle Eastern (MID) AF: 0.745 AC: 219 AN: 294

European-Non Finnish (NFE) AF: 0.853 AC: 57988 AN: 68006

Other (OTH) AF: 0.727 AC: 1535 AN: 2110

Alfa AF: 0.810 Hom.: 17572

Bravo AF: 0.719

Asia WGS AF: 0.550 AC: 1917 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	4.9
DANN	Benign	0.83
PhyloP100		0.75

Splicing

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

Other links and lift over

dbSNP: rs13379489; hg19: chr15-92926751;