chr14-29569596-G-A

Position:

• chr14-29569596-G-A

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 0.0459 in 152,098 control chromosomes in the GnomAD database, including 182 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 0.046 (182 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.09

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0623 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: 0.0458 AC: 6968 AN: 151980 Hom.: 182 Cov.: 31

Gnomad AFR AF: 0.0552

Gnomad AMI AF: 0.0593

Gnomad AMR AF: 0.0658

Gnomad ASJ AF: 0.0421

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.0297

Gnomad FIN AF: 0.0308

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.0428

Gnomad OTH AF: 0.0422

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

GnomAD4 genome AF: 0.0459 AC: 6979 AN: 152098 Hom.: 182 Cov.: 31 AF XY: 0.0450 AC XY: 3347 AN XY: 74360

Gnomad4 AFR AF: 0.0553

Gnomad4 AMR AF: 0.0657

Gnomad4 ASJ AF: 0.0421

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.0299

Gnomad4 FIN AF: 0.0308

Gnomad4 NFE AF: 0.0428

Gnomad4 OTH AF: 0.0417

Alfa AF: 0.0495 Hom.: 29

Bravo AF: 0.0489

Asia WGS AF: 0.0210 AC: 74 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.18
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: rs17114954; hg19: chr14-30038802;