chr14-63202929-A-G

Variant names:

• chr14-63202929-A-G
• rs1957779

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 0.503 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
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.608 AC: 25195 AN: 41450

American (AMR) AF: 0.405 AC: 6195 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.493 AC: 1710 AN: 3468

East Asian (EAS) AF: 0.626 AC: 3237 AN: 5174

South Asian (SAS) AF: 0.279 AC: 1342 AN: 4810

European-Finnish (FIN) AF: 0.492 AC: 5193 AN: 10552

Middle Eastern (MID) AF: 0.350 AC: 103 AN: 294

European-Non Finnish (NFE) AF: 0.470 AC: 31928 AN: 67948

Other (OTH) AF: 0.494 AC: 1045 AN: 2114

Alfa AF: 0.484 Hom.: 10500

Bravo AF: 0.504

Asia WGS AF: 0.472 AC: 1639 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.64
DANN	Benign	0.43
PhyloP100		-0.67

Splicing

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

Other links and lift over

dbSNP: rs1957779; hg19: chr14-63669647;