chr13-23902100-G-C

Variant names:

• chr13-23902100-G-C
• rs9551019

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 0.205 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
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	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

African (AFR) AF: 0.0778 AC: 3228 AN: 41492

American (AMR) AF: 0.231 AC: 3534 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.265 AC: 920 AN: 3468

East Asian (EAS) AF: 0.488 AC: 2524 AN: 5168

South Asian (SAS) AF: 0.130 AC: 624 AN: 4818

European-Finnish (FIN) AF: 0.320 AC: 3377 AN: 10566

Middle Eastern (MID) AF: 0.211 AC: 62 AN: 294

European-Non Finnish (NFE) AF: 0.238 AC: 16159 AN: 67980

Other (OTH) AF: 0.227 AC: 479 AN: 2106

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.62
DANN	Benign	0.76
PhyloP100		-0.45
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs9551019; hg19: chr13-24476239;