14-63202929-A-G

Variant names:

• chr14-63202929-A-G
• rs1957779

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 0.503 in 151,998 control chromosomes in the GnomAD database, including 19,763 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 0.50 (19763 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.667

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.608 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.502 AC: 76279 AN: 151882 Hom.: 19719 Cov.: 31

Gnomad AFR AF: 0.607

Gnomad AMI AF: 0.479

Gnomad AMR AF: 0.406

Gnomad ASJ AF: 0.493

Gnomad EAS AF: 0.625

Gnomad SAS AF: 0.279

Gnomad FIN AF: 0.492

Gnomad MID AF: 0.342

Gnomad NFE AF: 0.470

Gnomad OTH AF: 0.491

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

GnomAD4 genome AF: 0.503 AC: 76384 AN: 151998 Hom.: 19763 Cov.: 31 AF XY: 0.500 AC XY: 37144 AN XY: 74292

Gnomad4 AFR AF: 0.608

Gnomad4 AMR AF: 0.405

Gnomad4 ASJ AF: 0.493

Gnomad4 EAS AF: 0.626

Gnomad4 SAS AF: 0.279

Gnomad4 FIN AF: 0.492

Gnomad4 NFE AF: 0.470

Gnomad4 OTH AF: 0.494

Alfa AF: 0.479 Hom.: 4926

Bravo AF: 0.504

Asia WGS AF: 0.472 AC: 1639 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.64
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1957779; hg19: chr14-63669647;