rs9578521

Variant names:

• chr13-22999820-G-A
• rs9578521

Your query was ambiguous. Multiple possible variants found:

• chr13-22999820-G-A
• chr13-22999820-G-C

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 0.32 in 152,086 control chromosomes in the GnomAD database, including 9,268 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 0.32 (9268 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00400
• Publications: 1 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 (NFE) allele frequency at 95% confidence interval = 0.436 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: 0.320 AC: 48589 AN: 151968 Hom.: 9267 Cov.: 33

Gnomad AFR AF: 0.155

Gnomad AMI AF: 0.333

Gnomad AMR AF: 0.268

Gnomad ASJ AF: 0.453

Gnomad EAS AF: 0.0135

Gnomad SAS AF: 0.247

Gnomad FIN AF: 0.391

Gnomad MID AF: 0.366

Gnomad NFE AF: 0.440

Gnomad OTH AF: 0.362

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

GnomAD4 genome AF: 0.320 AC: 48601 AN: 152086 Hom.: 9268 Cov.: 33 AF XY: 0.313 AC XY: 23255 AN XY: 74348

African (AFR) AF: 0.155 AC: 6443 AN: 41494

American (AMR) AF: 0.268 AC: 4088 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.453 AC: 1573 AN: 3472

East Asian (EAS) AF: 0.0137 AC: 71 AN: 5180

South Asian (SAS) AF: 0.248 AC: 1192 AN: 4816

European-Finnish (FIN) AF: 0.391 AC: 4129 AN: 10550

Middle Eastern (MID) AF: 0.360 AC: 105 AN: 292

European-Non Finnish (NFE) AF: 0.440 AC: 29944 AN: 67984

Other (OTH) AF: 0.357 AC: 752 AN: 2106

Alfa AF: 0.375 Hom.: 2512

Bravo AF: 0.303

Asia WGS AF: 0.119 AC: 420 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	5.3
DANN	Benign	0.73
PhyloP100		-0.0040

Splicing

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

Other links and lift over

dbSNP: rs9578521; hg19: chr13-23573959;