chr14-29569596-G-A

Variant names:

• chr14-29569596-G-A
• rs17114954

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.0553 AC: 2296 AN: 41494

American (AMR) AF: 0.0657 AC: 1003 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.0421 AC: 146 AN: 3468

East Asian (EAS) AF: 0.00 AC: 0 AN: 5176

South Asian (SAS) AF: 0.0299 AC: 144 AN: 4812

European-Finnish (FIN) AF: 0.0308 AC: 326 AN: 10572

Middle Eastern (MID) AF: 0.0374 AC: 11 AN: 294

European-Non Finnish (NFE) AF: 0.0428 AC: 2911 AN: 67996

Other (OTH) AF: 0.0417 AC: 88 AN: 2108

Alfa AF: 0.0494 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
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs17114954; hg19: chr14-30038802;