13-108429276-A-G

Variant names:

• chr13-108429276-A-G
• rs7139897
• ENST00000636252.1:n.334-17906A>G

Variant summary

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

The ENST00000636252.1(ENSG00000283384):​n.334-17906A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.667 in 151,872 control chromosomes in the GnomAD database, including 33,901 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 0.67 (33901 hom., cov: 30)
• Consequence: ENSG00000283384 ENST00000636252.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.597
• Publications: 5 publications found

Genes affected

ENSG00000283384 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.701 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000636252.1. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000283384	ENST00000636252.1	TSL:5	n.334-17906A>G		intron	N/A
	ENSG00000283384	ENST00000637731.1	TSL:5	n.476-2195A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.667 AC: 101190 AN: 151752 Hom.: 33877 Cov.: 30

Gnomad AFR AF: 0.636

Gnomad AMI AF: 0.746

Gnomad AMR AF: 0.712

Gnomad ASJ AF: 0.730

Gnomad EAS AF: 0.489

Gnomad SAS AF: 0.666

Gnomad FIN AF: 0.590

Gnomad MID AF: 0.717

Gnomad NFE AF: 0.695

Gnomad OTH AF: 0.684

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

GnomAD4 genome AF: 0.667 AC: 101256 AN: 151872 Hom.: 33901 Cov.: 30 AF XY: 0.660 AC XY: 48955 AN XY: 74158

African (AFR) AF: 0.636 AC: 26343 AN: 41426

American (AMR) AF: 0.712 AC: 10876 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.730 AC: 2533 AN: 3470

East Asian (EAS) AF: 0.490 AC: 2510 AN: 5120

South Asian (SAS) AF: 0.666 AC: 3200 AN: 4802

European-Finnish (FIN) AF: 0.590 AC: 6213 AN: 10530

Middle Eastern (MID) AF: 0.702 AC: 205 AN: 292

European-Non Finnish (NFE) AF: 0.695 AC: 47250 AN: 67942

Other (OTH) AF: 0.687 AC: 1449 AN: 2110

Alfa AF: 0.694 Hom.: 61683

Bravo AF: 0.675

Asia WGS AF: 0.595 AC: 2070 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.85
DANN	Benign	0.32
PhyloP100		-0.60

Splicing

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

Other links and lift over

dbSNP: rs7139897; hg19: chr13-109081624;