13-88399285-T-G

Variant names:

• chr13-88399285-T-G
• rs1020684

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.711 in 151,966 control chromosomes in the GnomAD database, including 38,730 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 0.71 (38730 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.793
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.776 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.711 AC: 107995 AN: 151850 Hom.: 38714 Cov.: 32

Gnomad AFR AF: 0.750

Gnomad AMI AF: 0.743

Gnomad AMR AF: 0.787

Gnomad ASJ AF: 0.680

Gnomad EAS AF: 0.597

Gnomad SAS AF: 0.642

Gnomad FIN AF: 0.646

Gnomad MID AF: 0.763

Gnomad NFE AF: 0.695

Gnomad OTH AF: 0.722

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

GnomAD4 genome AF: 0.711 AC: 108058 AN: 151966 Hom.: 38730 Cov.: 32 AF XY: 0.709 AC XY: 52638 AN XY: 74236

African (AFR) AF: 0.750 AC: 31076 AN: 41462

American (AMR) AF: 0.788 AC: 12018 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.680 AC: 2357 AN: 3468

East Asian (EAS) AF: 0.596 AC: 3063 AN: 5138

South Asian (SAS) AF: 0.641 AC: 3085 AN: 4810

European-Finnish (FIN) AF: 0.646 AC: 6818 AN: 10558

Middle Eastern (MID) AF: 0.765 AC: 225 AN: 294

European-Non Finnish (NFE) AF: 0.695 AC: 47219 AN: 67966

Other (OTH) AF: 0.723 AC: 1521 AN: 2104

Alfa AF: 0.683 Hom.: 17475

Bravo AF: 0.723

Asia WGS AF: 0.637 AC: 2214 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.5
DANN	Benign	0.59
PhyloP100		-0.79

Splicing

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

Other links and lift over

dbSNP: rs1020684; hg19: chr13-89051540;