chr15-45975700-A-T

Variant names:

• chr15-45975700-A-T
• rs939394
• ENST00000773915.1:n.111+26512A>T

Variant summary

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

The ENST00000773915.1(ENSG00000300769):​n.111+26512A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.337 in 152,042 control chromosomes in the GnomAD database, including 11,129 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 0.34 (11129 hom., cov: 32)
• Consequence: ENSG00000300769 ENST00000773915.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.312
• Publications: 1 publications found

Genes affected

ENSG00000300769 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.609 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
ENSG00000300769	ENST00000773915.1	n.111+26512A>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.337 AC: 51227 AN: 151922 Hom.: 11096 Cov.: 32

Gnomad AFR AF: 0.615

Gnomad AMI AF: 0.226

Gnomad AMR AF: 0.210

Gnomad ASJ AF: 0.251

Gnomad EAS AF: 0.0137

Gnomad SAS AF: 0.177

Gnomad FIN AF: 0.276

Gnomad MID AF: 0.282

Gnomad NFE AF: 0.250

Gnomad OTH AF: 0.280

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

GnomAD4 genome AF: 0.337 AC: 51302 AN: 152042 Hom.: 11129 Cov.: 32 AF XY: 0.332 AC XY: 24681 AN XY: 74334

African (AFR) AF: 0.616 AC: 25519 AN: 41456

American (AMR) AF: 0.209 AC: 3198 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.251 AC: 870 AN: 3470

East Asian (EAS) AF: 0.0135 AC: 70 AN: 5170

South Asian (SAS) AF: 0.178 AC: 856 AN: 4816

European-Finnish (FIN) AF: 0.276 AC: 2922 AN: 10582

Middle Eastern (MID) AF: 0.289 AC: 85 AN: 294

European-Non Finnish (NFE) AF: 0.250 AC: 16990 AN: 67964

Other (OTH) AF: 0.278 AC: 586 AN: 2110

Alfa AF: 0.316 Hom.: 1146

Bravo AF: 0.341

Asia WGS AF: 0.128 AC: 446 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.92
DANN	Benign	0.50
PhyloP100		-0.31

Splicing

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

Other links and lift over

dbSNP: rs939394; hg19: chr15-46267898;