rs10521453

Variant names:

• chr9-73422600-G-A
• rs10521453
• ENST00000715869.1:n.216-3002G>A

Variant summary

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

The ENST00000715869.1(ENSG00000293608):​n.216-3002G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0272 in 151,856 control chromosomes in the GnomAD database, including 91 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 0.027 (91 hom., cov: 32)
• Consequence: ENSG00000293608 ENST00000715869.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.796
• Publications: 1 publications found

Genes affected

ENSG00000293608 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.064 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105376083	XR_001746729.1	n.994+499C>T		intron_variant	Intron 4 of 6
LOC105376084	XR_007061581.1	n.90-3002G>A		intron_variant	Intron 1 of 6
LOC105376084	XR_929939.1	n.90-3002G>A		intron_variant	Intron 1 of 4
LOC105376084	XR_929941.2	n.90-3002G>A		intron_variant	Intron 1 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000293608	ENST00000715869.1	n.216-3002G>A		intron_variant	Intron 2 of 4
ENSG00000293609	ENST00000715870.1	n.994+499C>T		intron_variant	Intron 4 of 6
ENSG00000293608	ENST00000726719.1	n.1065-3002G>A		intron_variant	Intron 9 of 12

Frequencies

GnomAD3 genomes AF: 0.0272 AC: 4126 AN: 151738 Hom.: 93 Cov.: 32

Gnomad AFR AF: 0.0661

Gnomad AMI AF: 0.00877

Gnomad AMR AF: 0.0194

Gnomad ASJ AF: 0.00894

Gnomad EAS AF: 0.0258

Gnomad SAS AF: 0.0311

Gnomad FIN AF: 0.00236

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0102

Gnomad OTH AF: 0.0225

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

GnomAD4 genome AF: 0.0272 AC: 4125 AN: 151856 Hom.: 91 Cov.: 32 AF XY: 0.0267 AC XY: 1979 AN XY: 74204

African (AFR) AF: 0.0661 AC: 2739 AN: 41458

American (AMR) AF: 0.0194 AC: 295 AN: 15222

Ashkenazi Jewish (ASJ) AF: 0.00894 AC: 31 AN: 3466

East Asian (EAS) AF: 0.0249 AC: 128 AN: 5136

South Asian (SAS) AF: 0.0309 AC: 149 AN: 4824

European-Finnish (FIN) AF: 0.00236 AC: 25 AN: 10608

Middle Eastern (MID) AF: 0.0374 AC: 11 AN: 294

European-Non Finnish (NFE) AF: 0.0102 AC: 692 AN: 67828

Other (OTH) AF: 0.0223 AC: 47 AN: 2108

Alfa AF: 0.0205 Hom.: 11

Bravo AF: 0.0290

Asia WGS AF: 0.0430 AC: 151 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.57
DANN	Benign	0.28
PhyloP100		-0.80

Splicing

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

Other links and lift over

dbSNP: rs10521453; hg19: chr9-76037516;