14-57998268-G-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 0.512 in 151,914 control chromosomes in the GnomAD database, including 20,105 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 0.51 (20105 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.914

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.629 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: 0.512 AC: 77745 AN: 151796 Hom.: 20071 Cov.: 32

Gnomad AFR AF: 0.480

Gnomad AMI AF: 0.433

Gnomad AMR AF: 0.502

Gnomad ASJ AF: 0.483

Gnomad EAS AF: 0.648

Gnomad SAS AF: 0.432

Gnomad FIN AF: 0.535

Gnomad MID AF: 0.456

Gnomad NFE AF: 0.529

Gnomad OTH AF: 0.489

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

GnomAD4 genome AF: 0.512 AC: 77837 AN: 151914 Hom.: 20105 Cov.: 32 AF XY: 0.512 AC XY: 37970 AN XY: 74228

Gnomad4 AFR AF: 0.481

Gnomad4 AMR AF: 0.502

Gnomad4 ASJ AF: 0.483

Gnomad4 EAS AF: 0.647

Gnomad4 SAS AF: 0.433

Gnomad4 FIN AF: 0.535

Gnomad4 NFE AF: 0.529

Gnomad4 OTH AF: 0.495

Alfa AF: 0.520 Hom.: 2456

Bravo AF: 0.509

Asia WGS AF: 0.536 AC: 1869 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	1.7
Dann	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2747100; hg19: chr14-58464986;