15-53409901-G-A

Variant names:

• chr15-53409901-G-A
• rs10518721
• ENST00000772669.1:n.289-1673G>A

Variant summary

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

The ENST00000772669.1(ENSG00000300550):​n.289-1673G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.234 in 151,978 control chromosomes in the GnomAD database, including 5,012 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 0.23 (5012 hom., cov: 32)
• Consequence: ENSG00000300550 ENST00000772669.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.83
• Publications: 2 publications found

Genes affected

ENSG00000300550 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.326 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
ENSG00000300550	ENST00000772669.1	n.289-1673G>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.234 AC: 35602 AN: 151860 Hom.: 5015 Cov.: 32

Gnomad AFR AF: 0.0785

Gnomad AMI AF: 0.264

Gnomad AMR AF: 0.273

Gnomad ASJ AF: 0.404

Gnomad EAS AF: 0.135

Gnomad SAS AF: 0.340

Gnomad FIN AF: 0.297

Gnomad MID AF: 0.288

Gnomad NFE AF: 0.302

Gnomad OTH AF: 0.245

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

GnomAD4 genome AF: 0.234 AC: 35593 AN: 151978 Hom.: 5012 Cov.: 32 AF XY: 0.236 AC XY: 17515 AN XY: 74270

African (AFR) AF: 0.0783 AC: 3247 AN: 41494

American (AMR) AF: 0.273 AC: 4167 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.404 AC: 1400 AN: 3464

East Asian (EAS) AF: 0.135 AC: 698 AN: 5158

South Asian (SAS) AF: 0.340 AC: 1630 AN: 4798

European-Finnish (FIN) AF: 0.297 AC: 3132 AN: 10548

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

European-Non Finnish (NFE) AF: 0.302 AC: 20483 AN: 67924

Other (OTH) AF: 0.242 AC: 511 AN: 2110

Alfa AF: 0.271 Hom.: 1292

Bravo AF: 0.223

Asia WGS AF: 0.250 AC: 868 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.029
DANN	Benign	0.51
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs10518721; hg19: chr15-53702098;