chr13-99122393-G-A

Variant names:

• chr13-99122393-G-A
• rs11069349

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 0.191 in 152,112 control chromosomes in the GnomAD database, including 2,843 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 0.19 (2843 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.247
• Publications: 11 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.215 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: 0.191 AC: 29035 AN: 151994 Hom.: 2840 Cov.: 33

Gnomad AFR AF: 0.150

Gnomad AMI AF: 0.193

Gnomad AMR AF: 0.175

Gnomad ASJ AF: 0.121

Gnomad EAS AF: 0.153

Gnomad SAS AF: 0.181

Gnomad FIN AF: 0.248

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.218

Gnomad OTH AF: 0.189

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

GnomAD4 genome AF: 0.191 AC: 29039 AN: 152112 Hom.: 2843 Cov.: 33 AF XY: 0.191 AC XY: 14223 AN XY: 74358

African (AFR) AF: 0.150 AC: 6235 AN: 41522

American (AMR) AF: 0.175 AC: 2675 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.121 AC: 419 AN: 3466

East Asian (EAS) AF: 0.153 AC: 790 AN: 5168

South Asian (SAS) AF: 0.179 AC: 864 AN: 4816

European-Finnish (FIN) AF: 0.248 AC: 2623 AN: 10560

Middle Eastern (MID) AF: 0.156 AC: 46 AN: 294

European-Non Finnish (NFE) AF: 0.218 AC: 14812 AN: 67972

Other (OTH) AF: 0.189 AC: 399 AN: 2110

Alfa AF: 0.204 Hom.: 10306

Bravo AF: 0.182

Asia WGS AF: 0.180 AC: 627 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.7
DANN	Benign	0.21
PhyloP100		-0.25

Splicing

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

Other links and lift over

dbSNP: rs11069349; hg19: chr13-99774647;