chr13-104869384-A-T

Position:

• chr13-104869384-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 0.344 in 152,012 control chromosomes in the GnomAD database, including 9,297 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 0.34 (9297 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.876

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.475 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.104869384A>T		intergenic_region
LOC107984608	XR_001749997.2	n.128-20913A>T		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.343 AC: 52162 AN: 151894 Hom.: 9281 Cov.: 32

Gnomad AFR AF: 0.414

Gnomad AMI AF: 0.300

Gnomad AMR AF: 0.304

Gnomad ASJ AF: 0.223

Gnomad EAS AF: 0.490

Gnomad SAS AF: 0.376

Gnomad FIN AF: 0.335

Gnomad MID AF: 0.316

Gnomad NFE AF: 0.305

Gnomad OTH AF: 0.301

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

GnomAD4 genome AF: 0.344 AC: 52220 AN: 152012 Hom.: 9297 Cov.: 32 AF XY: 0.345 AC XY: 25655 AN XY: 74290

Gnomad4 AFR AF: 0.414

Gnomad4 AMR AF: 0.303

Gnomad4 ASJ AF: 0.223

Gnomad4 EAS AF: 0.491

Gnomad4 SAS AF: 0.375

Gnomad4 FIN AF: 0.335

Gnomad4 NFE AF: 0.305

Gnomad4 OTH AF: 0.304

Alfa AF: 0.328 Hom.: 1078

Bravo AF: 0.344

Asia WGS AF: 0.408 AC: 1420 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	6.3
DANN	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3916951; hg19: chr13-105521735;