rs4899260

Positions:

• chr14-68811487-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 0.272 in 152,166 control chromosomes in the GnomAD database, including 6,339 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 0.27 (6339 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.214

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.38 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: 0.272 AC: 41317 AN: 152048 Hom.: 6336 Cov.: 33

Gnomad AFR AF: 0.385

Gnomad AMI AF: 0.242

Gnomad AMR AF: 0.200

Gnomad ASJ AF: 0.248

Gnomad EAS AF: 0.00212

Gnomad SAS AF: 0.188

Gnomad FIN AF: 0.224

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.255

Gnomad OTH AF: 0.253

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

GnomAD4 genome AF: 0.272 AC: 41339 AN: 152166 Hom.: 6339 Cov.: 33 AF XY: 0.265 AC XY: 19685 AN XY: 74404

Gnomad4 AFR AF: 0.385

Gnomad4 AMR AF: 0.199

Gnomad4 ASJ AF: 0.248

Gnomad4 EAS AF: 0.00212

Gnomad4 SAS AF: 0.187

Gnomad4 FIN AF: 0.224

Gnomad4 NFE AF: 0.255

Gnomad4 OTH AF: 0.250

Alfa AF: 0.251 Hom.: 8246

Bravo AF: 0.274

Asia WGS AF: 0.104 AC: 365 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	8.9
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4899260; hg19: chr14-69278204;