rs10517288

Variant names:

• chr4-33644184-C-A
• rs10517288
• ENST00000673514.1:n.1365-49173C>A

Your query was ambiguous. Multiple possible variants found:

• chr4-33644184-C-A
• chr4-33644184-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000673514.1(ENSG00000288321):​n.1365-49173C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0292 in 151,758 control chromosomes in the GnomAD database, including 86 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 0.029 (86 hom., cov: 32)
• Consequence: ENSG00000288321 ENST00000673514.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.644

Genes affected

ENSG00000288321 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0584 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.1365-49173C>A		intron_variant	Intron 8 of 8

Frequencies

GnomAD3 genomes AF: 0.0292 AC: 4422 AN: 151640 Hom.: 86 Cov.: 32

Gnomad AFR AF: 0.0604

Gnomad AMI AF: 0.0164

Gnomad AMR AF: 0.0149

Gnomad ASJ AF: 0.00521

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00663

Gnomad FIN AF: 0.0623

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.0137

Gnomad OTH AF: 0.0192

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

GnomAD4 genome AF: 0.0292 AC: 4426 AN: 151758 Hom.: 86 Cov.: 32 AF XY: 0.0310 AC XY: 2302 AN XY: 74170

Gnomad4 AFR AF: 0.0603

Gnomad4 AMR AF: 0.0149

Gnomad4 ASJ AF: 0.00521

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00663

Gnomad4 FIN AF: 0.0623

Gnomad4 NFE AF: 0.0137

Gnomad4 OTH AF: 0.0190

Alfa AF: 0.0149 Hom.: 21

Bravo AF: 0.0274

Asia WGS AF: 0.0120 AC: 41 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	0.51
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10517288; hg19: chr4-33645806;