chr13-43904864-A-G

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 12 publications found

Genes affected

ENSG00000281883 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000627615.1. 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
	ENSG00000281883	ENST00000627615.1	TSL:5	n.*285-2016A>G		intron	N/A	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

African (AFR) AF: 0.0863 AC: 3588 AN: 41574

American (AMR) AF: 0.126 AC: 1932 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.134 AC: 466 AN: 3470

East Asian (EAS) AF: 0.284 AC: 1470 AN: 5180

South Asian (SAS) AF: 0.246 AC: 1185 AN: 4812

European-Finnish (FIN) AF: 0.174 AC: 1839 AN: 10596

Middle Eastern (MID) AF: 0.160 AC: 47 AN: 294

European-Non Finnish (NFE) AF: 0.105 AC: 7138 AN: 67962

Other (OTH) AF: 0.130 AC: 275 AN: 2116

Alfa AF: 0.111 Hom.: 807

Bravo AF: 0.110

Asia WGS AF: 0.330 AC: 1147 AN: 3478

ClinVar

ClinVar submissions as Germline

Significance: Uncertain risk allele

Revision: no assertion criteria provided

Pathogenic	VUS	Benign	Condition
-	1	-	Leprosy, susceptibility to, 1 (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	5.7
DANN	Benign	0.51
PhyloP100		0.50

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

Other links and lift over

dbSNP: rs10507522; hg19: chr13-44479000;