rs7139897

Positions:

• chr13-108429276-A-G
• chr13-108429276-A-T

Variant summary

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

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: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.597

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.108429276A>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000283384	ENST00000636252.1	n.334-17906A>G		intron_variant		5
ENSG00000283384	ENST00000637731.1	n.476-2195A>G		intron_variant		5

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

Gnomad4 AFR AF: 0.636

Gnomad4 AMR AF: 0.712

Gnomad4 ASJ AF: 0.730

Gnomad4 EAS AF: 0.490

Gnomad4 SAS AF: 0.666

Gnomad4 FIN AF: 0.590

Gnomad4 NFE AF: 0.695

Gnomad4 OTH AF: 0.687

Alfa AF: 0.696 Hom.: 48695

Bravo AF: 0.675

Asia WGS AF: 0.595 AC: 2070 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7139897; hg19: chr13-109081624;