chr14-89787552-C-T

Position:

• chr14-89787552-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 0.371 in 152,138 control chromosomes in the GnomAD database, including 11,437 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 (11437 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.14

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.453 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: 0.371 AC: 56405 AN: 152020 Hom.: 11442 Cov.: 33

Gnomad AFR AF: 0.260

Gnomad AMI AF: 0.457

Gnomad AMR AF: 0.355

Gnomad ASJ AF: 0.419

Gnomad EAS AF: 0.0310

Gnomad SAS AF: 0.335

Gnomad FIN AF: 0.433

Gnomad MID AF: 0.487

Gnomad NFE AF: 0.457

Gnomad OTH AF: 0.382

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

GnomAD4 genome AF: 0.371 AC: 56408 AN: 152138 Hom.: 11437 Cov.: 33 AF XY: 0.367 AC XY: 27268 AN XY: 74384

Gnomad4 AFR AF: 0.259

Gnomad4 AMR AF: 0.355

Gnomad4 ASJ AF: 0.419

Gnomad4 EAS AF: 0.0314

Gnomad4 SAS AF: 0.334

Gnomad4 FIN AF: 0.433

Gnomad4 NFE AF: 0.457

Gnomad4 OTH AF: 0.382

Alfa AF: 0.437 Hom.: 20202

Bravo AF: 0.361

Asia WGS AF: 0.178 AC: 622 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.059
DANN	Benign	0.18

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8016216; hg19: chr14-90253896;