chr13-20196390-A-T

Variant names:

• chr13-20196390-A-T
• rs9552102

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 0.108 in 152,264 control chromosomes in the GnomAD database, including 1,382 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 0.11 (1382 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0150
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.403 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: 0.108 AC: 16387 AN: 152148 Hom.: 1381 Cov.: 32

Gnomad AFR AF: 0.131

Gnomad AMI AF: 0.0779

Gnomad AMR AF: 0.201

Gnomad ASJ AF: 0.0948

Gnomad EAS AF: 0.418

Gnomad SAS AF: 0.0741

Gnomad FIN AF: 0.0323

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.0639

Gnomad OTH AF: 0.113

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

GnomAD4 genome AF: 0.108 AC: 16410 AN: 152264 Hom.: 1382 Cov.: 32 AF XY: 0.112 AC XY: 8306 AN XY: 74438

African (AFR) AF: 0.131 AC: 5442 AN: 41536

American (AMR) AF: 0.202 AC: 3084 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0948 AC: 329 AN: 3470

East Asian (EAS) AF: 0.418 AC: 2160 AN: 5166

South Asian (SAS) AF: 0.0741 AC: 358 AN: 4830

European-Finnish (FIN) AF: 0.0323 AC: 343 AN: 10620

Middle Eastern (MID) AF: 0.133 AC: 39 AN: 294

European-Non Finnish (NFE) AF: 0.0639 AC: 4347 AN: 68032

Other (OTH) AF: 0.112 AC: 237 AN: 2110

Alfa AF: 0.0859 Hom.: 92

Bravo AF: 0.126

Asia WGS AF: 0.209 AC: 725 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	6.4
DANN	Benign	0.79
PhyloP100		-0.015

Splicing

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

Other links and lift over

dbSNP: rs9552102; hg19: chr13-20770529;