5-100199236-C-T

Variant names:

• chr5-100199236-C-T
• rs10053097

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 151,286 control chromosomes in the GnomAD database, including 7,962 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 (7962 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.668
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.36 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: 0.319 AC: 48260 AN: 151168 Hom.: 7935 Cov.: 31

Gnomad AFR AF: 0.364

Gnomad AMI AF: 0.258

Gnomad AMR AF: 0.303

Gnomad ASJ AF: 0.379

Gnomad EAS AF: 0.0522

Gnomad SAS AF: 0.123

Gnomad FIN AF: 0.317

Gnomad MID AF: 0.323

Gnomad NFE AF: 0.327

Gnomad OTH AF: 0.356

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

GnomAD4 genome AF: 0.320 AC: 48338 AN: 151286 Hom.: 7962 Cov.: 31 AF XY: 0.314 AC XY: 23195 AN XY: 73954

African (AFR) AF: 0.365 AC: 15086 AN: 41338

American (AMR) AF: 0.302 AC: 4568 AN: 15108

Ashkenazi Jewish (ASJ) AF: 0.379 AC: 1311 AN: 3458

East Asian (EAS) AF: 0.0521 AC: 268 AN: 5144

South Asian (SAS) AF: 0.123 AC: 592 AN: 4818

European-Finnish (FIN) AF: 0.317 AC: 3351 AN: 10576

Middle Eastern (MID) AF: 0.330 AC: 97 AN: 294

European-Non Finnish (NFE) AF: 0.327 AC: 22091 AN: 67544

Other (OTH) AF: 0.353 AC: 739 AN: 2096

Alfa AF: 0.328 Hom.: 1039

Bravo AF: 0.323

Asia WGS AF: 0.129 AC: 454 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.30
DANN	Benign	0.33
PhyloP100		-0.67

Splicing

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

Other links and lift over

dbSNP: rs10053097; hg19: chr5-99534940;