ENST00000773301.1:n.266+3724A>G

Variant names:

• chr15-79094024-A-G
• rs1443658
• ENST00000773301.1:n.266+3724A>G

Variant summary

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

The ENST00000773301.1(ENSG00000300669):​n.266+3724A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.522 in 151,824 control chromosomes in the GnomAD database, including 22,826 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 0.52 (22826 hom., cov: 30)
• Consequence: ENSG00000300669 ENST00000773301.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.999
• Publications: 4 publications found

Genes affected

ENSG00000300669 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.766 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
ENSG00000300669	ENST00000773301.1	n.266+3724A>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.522 AC: 79163 AN: 151706 Hom.: 22776 Cov.: 30

Gnomad AFR AF: 0.773

Gnomad AMI AF: 0.273

Gnomad AMR AF: 0.529

Gnomad ASJ AF: 0.375

Gnomad EAS AF: 0.546

Gnomad SAS AF: 0.260

Gnomad FIN AF: 0.403

Gnomad MID AF: 0.301

Gnomad NFE AF: 0.416

Gnomad OTH AF: 0.484

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

GnomAD4 genome AF: 0.522 AC: 79278 AN: 151824 Hom.: 22826 Cov.: 30 AF XY: 0.518 AC XY: 38467 AN XY: 74214

African (AFR) AF: 0.773 AC: 32005 AN: 41380

American (AMR) AF: 0.530 AC: 8084 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.375 AC: 1299 AN: 3462

East Asian (EAS) AF: 0.547 AC: 2815 AN: 5144

South Asian (SAS) AF: 0.260 AC: 1250 AN: 4810

European-Finnish (FIN) AF: 0.403 AC: 4245 AN: 10538

Middle Eastern (MID) AF: 0.307 AC: 89 AN: 290

European-Non Finnish (NFE) AF: 0.416 AC: 28228 AN: 67916

Other (OTH) AF: 0.481 AC: 1014 AN: 2110

Alfa AF: 0.413 Hom.: 5841

Bravo AF: 0.554

Asia WGS AF: 0.378 AC: 1315 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.48
DANN	Benign	0.55
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs1443658; hg19: chr15-79386366;