5-101522490-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 0.0661 in 151,712 control chromosomes in the GnomAD database, including 925 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 0.066 (925 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.80

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.204 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: 0.0660 AC: 10003 AN: 151592 Hom.: 921 Cov.: 32

Gnomad AFR AF: 0.207

Gnomad AMI AF: 0.0428

Gnomad AMR AF: 0.0341

Gnomad ASJ AF: 0.0291

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00540

Gnomad FIN AF: 0.000380

Gnomad MID AF: 0.0481

Gnomad NFE AF: 0.00913

Gnomad OTH AF: 0.0625

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

GnomAD4 genome AF: 0.0661 AC: 10034 AN: 151712 Hom.: 925 Cov.: 32 AF XY: 0.0645 AC XY: 4778 AN XY: 74118

Gnomad4 AFR AF: 0.207

Gnomad4 AMR AF: 0.0341

Gnomad4 ASJ AF: 0.0291

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00520

Gnomad4 FIN AF: 0.000380

Gnomad4 NFE AF: 0.00913

Gnomad4 OTH AF: 0.0618

Alfa AF: 0.00375 Hom.: 3

Bravo AF: 0.0768

Asia WGS AF: 0.0130 AC: 45 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.10
Dann	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10515310; hg19: chr5-100858194;