rs4899554

Positions:

• chr14-75234518-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 0.143 in 151,972 control chromosomes in the GnomAD database, including 1,857 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 0.14 (1857 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.516

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.185 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: 0.143 AC: 21681 AN: 151854 Hom.: 1846 Cov.: 31

Gnomad AFR AF: 0.0549

Gnomad AMI AF: 0.134

Gnomad AMR AF: 0.162

Gnomad ASJ AF: 0.126

Gnomad EAS AF: 0.185

Gnomad SAS AF: 0.132

Gnomad FIN AF: 0.167

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.187

Gnomad OTH AF: 0.129

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

GnomAD4 genome AF: 0.143 AC: 21710 AN: 151972 Hom.: 1857 Cov.: 31 AF XY: 0.141 AC XY: 10485 AN XY: 74258

Gnomad4 AFR AF: 0.0550

Gnomad4 AMR AF: 0.162

Gnomad4 ASJ AF: 0.126

Gnomad4 EAS AF: 0.185

Gnomad4 SAS AF: 0.132

Gnomad4 FIN AF: 0.167

Gnomad4 NFE AF: 0.187

Gnomad4 OTH AF: 0.135

Alfa AF: 0.174 Hom.: 1337

Bravo AF: 0.140

Asia WGS AF: 0.154 AC: 538 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.8
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4899554; hg19: chr14-75701221;