rs4703116

Positions:

• chr5-100793209-T-C

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 0.368 in 152,110 control chromosomes in the GnomAD database, including 10,751 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 0.37 (10751 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.55

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.431 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.368 AC: 55898 AN: 151992 Hom.: 10737 Cov.: 33

Gnomad AFR AF: 0.437

Gnomad AMI AF: 0.334

Gnomad AMR AF: 0.423

Gnomad ASJ AF: 0.262

Gnomad EAS AF: 0.189

Gnomad SAS AF: 0.239

Gnomad FIN AF: 0.372

Gnomad MID AF: 0.313

Gnomad NFE AF: 0.342

Gnomad OTH AF: 0.357

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

GnomAD4 genome AF: 0.368 AC: 55952 AN: 152110 Hom.: 10751 Cov.: 33 AF XY: 0.367 AC XY: 27309 AN XY: 74378

Gnomad4 AFR AF: 0.437

Gnomad4 AMR AF: 0.423

Gnomad4 ASJ AF: 0.262

Gnomad4 EAS AF: 0.189

Gnomad4 SAS AF: 0.240

Gnomad4 FIN AF: 0.372

Gnomad4 NFE AF: 0.342

Gnomad4 OTH AF: 0.355

Alfa AF: 0.339 Hom.: 17983

Bravo AF: 0.377

Asia WGS AF: 0.230 AC: 801 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.1
DANN	Benign	0.27

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4703116; hg19: chr5-100128913; COSMIC: COSV60170743;