14-98032614-A-G

Variant names:

• chr14-98032614-A-G
• rs4900384

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 0.4 in 152,066 control chromosomes in the GnomAD database, including 13,511 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 0.40 (13511 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.897
• Publications: 63 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.593 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.400 AC: 60766 AN: 151948 Hom.: 13485 Cov.: 32

Gnomad AFR AF: 0.569

Gnomad AMI AF: 0.175

Gnomad AMR AF: 0.369

Gnomad ASJ AF: 0.320

Gnomad EAS AF: 0.610

Gnomad SAS AF: 0.533

Gnomad FIN AF: 0.415

Gnomad MID AF: 0.303

Gnomad NFE AF: 0.285

Gnomad OTH AF: 0.385

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

GnomAD4 genome AF: 0.400 AC: 60844 AN: 152066 Hom.: 13511 Cov.: 32 AF XY: 0.410 AC XY: 30487 AN XY: 74338

African (AFR) AF: 0.569 AC: 23568 AN: 41448

American (AMR) AF: 0.369 AC: 5647 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.320 AC: 1112 AN: 3470

East Asian (EAS) AF: 0.611 AC: 3149 AN: 5156

South Asian (SAS) AF: 0.533 AC: 2565 AN: 4812

European-Finnish (FIN) AF: 0.415 AC: 4390 AN: 10590

Middle Eastern (MID) AF: 0.312 AC: 91 AN: 292

European-Non Finnish (NFE) AF: 0.285 AC: 19347 AN: 67984

Other (OTH) AF: 0.387 AC: 815 AN: 2108

Alfa AF: 0.324 Hom.: 38700

Bravo AF: 0.401

Asia WGS AF: 0.550 AC: 1910 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	5.3
DANN	Benign	0.80
PhyloP100		0.90

Splicing

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

Other links and lift over

dbSNP: rs4900384; hg19: chr14-98498951;