rs9551019

Variant names:

• chr13-23902100-G-C
• rs9551019

Your query was ambiguous. Multiple possible variants found:

• chr13-23902100-G-C
• chr13-23902100-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.205 in 152,096 control chromosomes in the GnomAD database, including 3,829 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 0.20 (3829 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.453

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.473 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: 0.205 AC: 31101 AN: 151978 Hom.: 3832 Cov.: 32

Gnomad AFR AF: 0.0777

Gnomad AMI AF: 0.217

Gnomad AMR AF: 0.231

Gnomad ASJ AF: 0.265

Gnomad EAS AF: 0.490

Gnomad SAS AF: 0.128

Gnomad FIN AF: 0.320

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.238

Gnomad OTH AF: 0.229

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

GnomAD4 genome AF: 0.205 AC: 31105 AN: 152096 Hom.: 3829 Cov.: 32 AF XY: 0.208 AC XY: 15470 AN XY: 74354

Gnomad4 AFR AF: 0.0778

Gnomad4 AMR AF: 0.231

Gnomad4 ASJ AF: 0.265

Gnomad4 EAS AF: 0.488

Gnomad4 SAS AF: 0.130

Gnomad4 FIN AF: 0.320

Gnomad4 NFE AF: 0.238

Gnomad4 OTH AF: 0.227

Alfa AF: 0.208 Hom.: 442

Bravo AF: 0.199

Asia WGS AF: 0.250 AC: 868 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.62
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9551019; hg19: chr13-24476239;