rs9519697

Variant names:

• chr13-105520380-A-G
• rs9519697

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 0.388 in 151,854 control chromosomes in the GnomAD database, including 13,215 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 0.39 (13215 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.792
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.506 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: 0.388 AC: 58948 AN: 151736 Hom.: 13204 Cov.: 30

Gnomad AFR AF: 0.153

Gnomad AMI AF: 0.523

Gnomad AMR AF: 0.515

Gnomad ASJ AF: 0.441

Gnomad EAS AF: 0.448

Gnomad SAS AF: 0.452

Gnomad FIN AF: 0.425

Gnomad MID AF: 0.481

Gnomad NFE AF: 0.484

Gnomad OTH AF: 0.397

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

GnomAD4 genome AF: 0.388 AC: 58980 AN: 151854 Hom.: 13215 Cov.: 30 AF XY: 0.391 AC XY: 29037 AN XY: 74220

African (AFR) AF: 0.153 AC: 6346 AN: 41478

American (AMR) AF: 0.515 AC: 7846 AN: 15222

Ashkenazi Jewish (ASJ) AF: 0.441 AC: 1529 AN: 3466

East Asian (EAS) AF: 0.448 AC: 2315 AN: 5166

South Asian (SAS) AF: 0.452 AC: 2175 AN: 4812

European-Finnish (FIN) AF: 0.425 AC: 4476 AN: 10532

Middle Eastern (MID) AF: 0.486 AC: 143 AN: 294

European-Non Finnish (NFE) AF: 0.484 AC: 32846 AN: 67864

Other (OTH) AF: 0.392 AC: 828 AN: 2110

Alfa AF: 0.428 Hom.: 2548

Bravo AF: 0.384

Asia WGS AF: 0.395 AC: 1372 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.3
DANN	Benign	0.53
PhyloP100		-0.79

Splicing

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

Other links and lift over

dbSNP: rs9519697; hg19: chr13-106172729;