13-85808985-G-A

Position:

• chr13-85808985-G-A

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 0.365 in 151,914 control chromosomes in the GnomAD database, including 11,493 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 0.37 (11493 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.304

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.592 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.365 AC: 55466 AN: 151796 Hom.: 11482 Cov.: 31

Gnomad AFR AF: 0.165

Gnomad AMI AF: 0.567

Gnomad AMR AF: 0.402

Gnomad ASJ AF: 0.358

Gnomad EAS AF: 0.609

Gnomad SAS AF: 0.429

Gnomad FIN AF: 0.432

Gnomad MID AF: 0.329

Gnomad NFE AF: 0.443

Gnomad OTH AF: 0.384

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

GnomAD4 genome AF: 0.365 AC: 55499 AN: 151914 Hom.: 11493 Cov.: 31 AF XY: 0.367 AC XY: 27242 AN XY: 74216

Gnomad4 AFR AF: 0.165

Gnomad4 AMR AF: 0.402

Gnomad4 ASJ AF: 0.358

Gnomad4 EAS AF: 0.610

Gnomad4 SAS AF: 0.429

Gnomad4 FIN AF: 0.432

Gnomad4 NFE AF: 0.443

Gnomad4 OTH AF: 0.385

Alfa AF: 0.387 Hom.: 3166

Bravo AF: 0.354

Asia WGS AF: 0.495 AC: 1719 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.3
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9531843; hg19: chr13-86383120;