13-84975601-T-G

Position:

• chr13-84975601-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 0.497 in 151,756 control chromosomes in the GnomAD database, including 19,293 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 0.50 (19293 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.254

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.672 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.84975601T>G		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.497 AC: 75357 AN: 151638 Hom.: 19263 Cov.: 32

Gnomad AFR AF: 0.565

Gnomad AMI AF: 0.449

Gnomad AMR AF: 0.575

Gnomad ASJ AF: 0.493

Gnomad EAS AF: 0.692

Gnomad SAS AF: 0.610

Gnomad FIN AF: 0.400

Gnomad MID AF: 0.411

Gnomad NFE AF: 0.432

Gnomad OTH AF: 0.486

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

GnomAD4 genome AF: 0.497 AC: 75442 AN: 151756 Hom.: 19293 Cov.: 32 AF XY: 0.501 AC XY: 37198 AN XY: 74180

Gnomad4 AFR AF: 0.565

Gnomad4 AMR AF: 0.575

Gnomad4 ASJ AF: 0.493

Gnomad4 EAS AF: 0.691

Gnomad4 SAS AF: 0.610

Gnomad4 FIN AF: 0.400

Gnomad4 NFE AF: 0.432

Gnomad4 OTH AF: 0.491

Alfa AF: 0.287 Hom.: 690

Bravo AF: 0.515

Asia WGS AF: 0.625 AC: 2165 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.8
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9531686; hg19: chr13-85549736;