rs10507522

Variant names:

• chr13-43904864-A-G
• rs10507522
• ENST00000627615.1:n.*285-2016A>G

Variant summary

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

The ENST00000627615.1(ENSG00000281883):​n.*285-2016A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.119 in 152,210 control chromosomes in the GnomAD database, including 1,263 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain risk allele (no stars).

• Frequency: Genomes: 𝑓 0.12 (1263 hom., cov: 32)
• Consequence: ENSG00000281883 ENST00000627615.1 intron
• Clinical Significance: Uncertain risk allele no assertion criteria provided O:1
• Conservation: PhyloP100: 0.503

Genes affected

ENSG00000281883 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.272 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
ENSG00000281883	ENST00000627615.1	n.*285-2016A>G		intron_variant	Intron 4 of 12	5		ENSP00000486083.1

Frequencies

GnomAD3 genomes AF: 0.119 AC: 18077 AN: 152092 Hom.: 1251 Cov.: 32

Gnomad AFR AF: 0.0859

Gnomad AMI AF: 0.186

Gnomad AMR AF: 0.126

Gnomad ASJ AF: 0.134

Gnomad EAS AF: 0.285

Gnomad SAS AF: 0.246

Gnomad FIN AF: 0.174

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.105

Gnomad OTH AF: 0.123

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

GnomAD4 genome AF: 0.119 AC: 18109 AN: 152210 Hom.: 1263 Cov.: 32 AF XY: 0.126 AC XY: 9410 AN XY: 74424

Gnomad4 AFR AF: 0.0863

Gnomad4 AMR AF: 0.126

Gnomad4 ASJ AF: 0.134

Gnomad4 EAS AF: 0.284

Gnomad4 SAS AF: 0.246

Gnomad4 FIN AF: 0.174

Gnomad4 NFE AF: 0.105

Gnomad4 OTH AF: 0.130

Alfa AF: 0.111 Hom.: 755

Bravo AF: 0.110

Asia WGS AF: 0.330 AC: 1147 AN: 3478

ClinVar

Significance: Uncertain risk allele

Submissions summary: Other:1

Revision: no assertion criteria provided

Submissions by phenotype

Leprosy, susceptibility to, 1 Other:1

Jun 10, 2022

Centro Dermatológico Federico Lleras Acosta, Hospital Universitario Centro Dermatológico Federico Lleras Acosta

Significance: Uncertain risk allele

Review Status: no assertion criteria provided

Collection Method: case-control

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	5.7
DANN	Benign	0.51

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs10507522; hg19: chr13-44479000;