rs10053097

chr5-100199236-C-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 0.32 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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	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

Gnomad4 AFR AF: 0.365

Gnomad4 AMR AF: 0.302

Gnomad4 ASJ AF: 0.379

Gnomad4 EAS AF: 0.0521

Gnomad4 SAS AF: 0.123

Gnomad4 FIN AF: 0.317

Gnomad4 NFE AF: 0.327

Gnomad4 OTH AF: 0.353

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.30
Dann	Benign	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10053097; hg19: chr5-99534940;