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. The variant received -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
• 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=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0584 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000673514.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000288321	ENST00000673514.1		n.1365-49173C>A		intron	N/A

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

African (AFR) AF: 0.0603 AC: 2503 AN: 41478

American (AMR) AF: 0.0149 AC: 226 AN: 15184

Ashkenazi Jewish (ASJ) AF: 0.00521 AC: 18 AN: 3458

East Asian (EAS) AF: 0.00 AC: 0 AN: 5154

South Asian (SAS) AF: 0.00663 AC: 32 AN: 4824

European-Finnish (FIN) AF: 0.0623 AC: 659 AN: 10572

Middle Eastern (MID) AF: 0.00680 AC: 2 AN: 294

European-Non Finnish (NFE) AF: 0.0137 AC: 931 AN: 67778

Other (OTH) AF: 0.0190 AC: 40 AN: 2104

Alfa AF: 0.0160 Hom.: 26

Bravo AF: 0.0274

Asia WGS AF: 0.0120 AC: 41 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.51
DANN	Benign	0.65
PhyloP100		-0.64

Splicing

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

Other links and lift over

dbSNP: rs10517288; hg19: chr4-33645806;