rs10517255

Variant names:

• chr4-32638404-C-A
• rs10517255
• ENST00000659320.1:n.216-53108G>T

Your query was ambiguous. Multiple possible variants found:

• chr4-32638404-C-A
• chr4-32638404-C-G

Variant summary

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

The ENST00000659320.1(ENSG00000286784):​n.216-53108G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.104 in 152,074 control chromosomes in the GnomAD database, including 2,041 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 0.10 (2041 hom., cov: 32)
• Consequence: ENSG00000286784 ENST00000659320.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0470
• Publications: 1 publications found

Genes affected

ENSG00000286784 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.287 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000659320.1. 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
	ENSG00000286784	ENST00000659320.1		n.216-53108G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.104 AC: 15804 AN: 151956 Hom.: 2039 Cov.: 32

Gnomad AFR AF: 0.291

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0718

Gnomad ASJ AF: 0.00433

Gnomad EAS AF: 0.269

Gnomad SAS AF: 0.0430

Gnomad FIN AF: 0.0284

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.00868

Gnomad OTH AF: 0.0759

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

GnomAD4 genome AF: 0.104 AC: 15831 AN: 152074 Hom.: 2041 Cov.: 32 AF XY: 0.103 AC XY: 7650 AN XY: 74372

African (AFR) AF: 0.291 AC: 12061 AN: 41432

American (AMR) AF: 0.0719 AC: 1099 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.00433 AC: 15 AN: 3468

East Asian (EAS) AF: 0.270 AC: 1389 AN: 5152

South Asian (SAS) AF: 0.0424 AC: 205 AN: 4830

European-Finnish (FIN) AF: 0.0284 AC: 301 AN: 10606

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

European-Non Finnish (NFE) AF: 0.00868 AC: 590 AN: 67986

Other (OTH) AF: 0.0751 AC: 159 AN: 2116

Alfa AF: 0.0234 Hom.: 114

Bravo AF: 0.118

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.84
DANN	Benign	0.40
PhyloP100		-0.047

Splicing

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

Other links and lift over

dbSNP: rs10517255; hg19: chr4-32640026;