rs1913208

Positions:

• chr13-104069439-T-G

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 0.53 in 151,880 control chromosomes in the GnomAD database, including 23,093 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 0.53 (23093 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.135

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.746 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.104069439T>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.530 AC: 80421 AN: 151762 Hom.: 23062 Cov.: 32

Gnomad AFR AF: 0.753

Gnomad AMI AF: 0.497

Gnomad AMR AF: 0.452

Gnomad ASJ AF: 0.446

Gnomad EAS AF: 0.358

Gnomad SAS AF: 0.362

Gnomad FIN AF: 0.367

Gnomad MID AF: 0.547

Gnomad NFE AF: 0.467

Gnomad OTH AF: 0.518

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

GnomAD4 genome AF: 0.530 AC: 80506 AN: 151880 Hom.: 23093 Cov.: 32 AF XY: 0.519 AC XY: 38490 AN XY: 74230

Gnomad4 AFR AF: 0.753

Gnomad4 AMR AF: 0.452

Gnomad4 ASJ AF: 0.446

Gnomad4 EAS AF: 0.358

Gnomad4 SAS AF: 0.361

Gnomad4 FIN AF: 0.367

Gnomad4 NFE AF: 0.467

Gnomad4 OTH AF: 0.517

Alfa AF: 0.471 Hom.: 34434

Bravo AF: 0.546

Asia WGS AF: 0.394 AC: 1373 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.1
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1913208; hg19: chr13-104721789;