rs10483517

Variant names:

• chr14-39755707-A-T
• rs10483517
• ENST00000650911.1:n.417+99899A>T

Variant summary

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

The ENST00000650911.1(ENSG00000258526):​n.417+99899A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.174 in 151,996 control chromosomes in the GnomAD database, including 2,537 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 0.17 (2537 hom., cov: 32)
• Consequence: ENSG00000258526 ENST00000650911.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.172
• Publications: 0 publications found

Genes affected

ENSG00000258526 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.392 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000650911.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000258526	ENST00000650911.1		n.417+99899A>T		intron	N/A
	ENSG00000258526	ENST00000651829.1		n.1323+43600A>T		intron	N/A
	ENSG00000258526	ENST00000652126.1		n.457+99899A>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.174 AC: 26488 AN: 151878 Hom.: 2541 Cov.: 32

Gnomad AFR AF: 0.182

Gnomad AMI AF: 0.0407

Gnomad AMR AF: 0.179

Gnomad ASJ AF: 0.122

Gnomad EAS AF: 0.408

Gnomad SAS AF: 0.128

Gnomad FIN AF: 0.238

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.150

Gnomad OTH AF: 0.159

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

GnomAD4 genome AF: 0.174 AC: 26483 AN: 151996 Hom.: 2537 Cov.: 32 AF XY: 0.177 AC XY: 13155 AN XY: 74280

African (AFR) AF: 0.182 AC: 7525 AN: 41452

American (AMR) AF: 0.179 AC: 2728 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.122 AC: 423 AN: 3470

East Asian (EAS) AF: 0.407 AC: 2097 AN: 5156

South Asian (SAS) AF: 0.127 AC: 613 AN: 4818

European-Finnish (FIN) AF: 0.238 AC: 2508 AN: 10550

Middle Eastern (MID) AF: 0.0884 AC: 26 AN: 294

European-Non Finnish (NFE) AF: 0.150 AC: 10192 AN: 67964

Other (OTH) AF: 0.158 AC: 334 AN: 2114

Alfa AF: 0.163 Hom.: 243

Bravo AF: 0.175

Asia WGS AF: 0.232 AC: 808 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.59
DANN	Benign	0.41
PhyloP100		-0.17

Splicing

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

Other links and lift over

dbSNP: rs10483517; hg19: chr14-40224911;