rs10517282

Variant names:

• chr4-33543548-G-A
• rs10517282
• ENST00000673514.1:n.459-23884G>A

Your query was ambiguous. Multiple possible variants found:

• chr4-33543548-G-A
• chr4-33543548-G-T

Variant summary

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

The ENST00000673514.1(ENSG00000288321):​n.459-23884G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0535 in 150,570 control chromosomes in the GnomAD database, including 418 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 0.054 (418 hom., cov: 32)
• Consequence: ENSG00000288321 ENST00000673514.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.220
• Publications: 0 publications found

Genes affected

ENSG00000288321 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.129 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
ENSG00000288321	ENST00000673514.1	n.459-23884G>A		intron_variant	Intron 2 of 8
ENSG00000288321	ENST00000822998.1	n.148-18247G>A		intron_variant	Intron 1 of 3
ENSG00000288321	ENST00000822999.1	n.119-23884G>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.0536 AC: 8060 AN: 150460 Hom.: 420 Cov.: 32

Gnomad AFR AF: 0.132

Gnomad AMI AF: 0.0307

Gnomad AMR AF: 0.0160

Gnomad ASJ AF: 0.0425

Gnomad EAS AF: 0.00895

Gnomad SAS AF: 0.0812

Gnomad FIN AF: 0.0503

Gnomad MID AF: 0.00955

Gnomad NFE AF: 0.0178

Gnomad OTH AF: 0.0323

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

GnomAD4 genome AF: 0.0535 AC: 8060 AN: 150570 Hom.: 418 Cov.: 32 AF XY: 0.0540 AC XY: 3960 AN XY: 73384

African (AFR) AF: 0.132 AC: 5436 AN: 41172

American (AMR) AF: 0.0160 AC: 242 AN: 15114

Ashkenazi Jewish (ASJ) AF: 0.0425 AC: 147 AN: 3456

East Asian (EAS) AF: 0.00897 AC: 46 AN: 5130

South Asian (SAS) AF: 0.0805 AC: 385 AN: 4784

European-Finnish (FIN) AF: 0.0503 AC: 506 AN: 10050

Middle Eastern (MID) AF: 0.0103 AC: 3 AN: 292

European-Non Finnish (NFE) AF: 0.0178 AC: 1200 AN: 67564

Other (OTH) AF: 0.0320 AC: 67 AN: 2096

Alfa AF: 0.0291 Hom.: 413

Bravo AF: 0.0513

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.72
DANN	Benign	0.53
PhyloP100		0.22

Splicing

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

Other links and lift over

dbSNP: rs10517282; hg19: chr4-33545170;