rs10483532

Variant names:

• chr14-39669396-T-G
• rs10483532
• ENST00000650911.1:n.417+13588T>G

Variant summary

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

The ENST00000650911.1(ENSG00000258526):​n.417+13588T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0236 in 152,246 control chromosomes in the GnomAD database, including 129 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 0.024 (129 hom., cov: 32)
• Consequence: ENSG00000258526 ENST00000650911.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.352
• Publications: 4 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=-0.73).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0959 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

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
	ENSG00000258526	ENST00000650911.1		n.417+13588T>G		intron	N/A
	ENSG00000258526	ENST00000651829.1		n.1196+13588T>G		intron	N/A
	ENSG00000258526	ENST00000652126.1		n.457+13588T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0236 AC: 3585 AN: 152130 Hom.: 127 Cov.: 32

Gnomad AFR AF: 0.00504

Gnomad AMI AF: 0.00548

Gnomad AMR AF: 0.0997

Gnomad ASJ AF: 0.0170

Gnomad EAS AF: 0.0767

Gnomad SAS AF: 0.0602

Gnomad FIN AF: 0.0193

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.0120

Gnomad OTH AF: 0.0353

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

GnomAD4 genome AF: 0.0236 AC: 3600 AN: 152246 Hom.: 129 Cov.: 32 AF XY: 0.0263 AC XY: 1958 AN XY: 74436

African (AFR) AF: 0.00503 AC: 209 AN: 41556

American (AMR) AF: 0.100 AC: 1527 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.0170 AC: 59 AN: 3468

East Asian (EAS) AF: 0.0771 AC: 400 AN: 5188

South Asian (SAS) AF: 0.0602 AC: 291 AN: 4830

European-Finnish (FIN) AF: 0.0193 AC: 205 AN: 10610

Middle Eastern (MID) AF: 0.0306 AC: 9 AN: 294

European-Non Finnish (NFE) AF: 0.0120 AC: 816 AN: 68010

Other (OTH) AF: 0.0373 AC: 79 AN: 2116

Alfa AF: 0.0197 Hom.: 260

Bravo AF: 0.0300

Asia WGS AF: 0.104 AC: 359 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	2.7
DANN	Benign	0.84
PhyloP100		-0.35

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs10483532;

hg19: chr14-40138600;