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. Variant got -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

Genes affected

ENSG00000288321 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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

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

Gnomad4 AFR AF: 0.132

Gnomad4 AMR AF: 0.0160

Gnomad4 ASJ AF: 0.0425

Gnomad4 EAS AF: 0.00897

Gnomad4 SAS AF: 0.0805

Gnomad4 FIN AF: 0.0503

Gnomad4 NFE AF: 0.0178

Gnomad4 OTH AF: 0.0320

Alfa AF: 0.0213 Hom.: 113

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10517282; hg19: chr4-33545170;