14-84200405-C-G

Variant names:

• chr14-84200405-C-G
• rs898939

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 0.62 in 152,008 control chromosomes in the GnomAD database, including 29,485 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 0.62 (29485 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.149
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.778 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: 0.620 AC: 94116 AN: 151890 Hom.: 29442 Cov.: 33

Gnomad AFR AF: 0.624

Gnomad AMI AF: 0.717

Gnomad AMR AF: 0.639

Gnomad ASJ AF: 0.700

Gnomad EAS AF: 0.798

Gnomad SAS AF: 0.721

Gnomad FIN AF: 0.475

Gnomad MID AF: 0.788

Gnomad NFE AF: 0.606

Gnomad OTH AF: 0.675

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

GnomAD4 genome AF: 0.620 AC: 94205 AN: 152008 Hom.: 29485 Cov.: 33 AF XY: 0.618 AC XY: 45924 AN XY: 74312

African (AFR) AF: 0.624 AC: 25883 AN: 41452

American (AMR) AF: 0.639 AC: 9764 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.700 AC: 2432 AN: 3472

East Asian (EAS) AF: 0.799 AC: 4129 AN: 5170

South Asian (SAS) AF: 0.721 AC: 3469 AN: 4814

European-Finnish (FIN) AF: 0.475 AC: 5019 AN: 10566

Middle Eastern (MID) AF: 0.789 AC: 232 AN: 294

European-Non Finnish (NFE) AF: 0.606 AC: 41202 AN: 67936

Other (OTH) AF: 0.674 AC: 1424 AN: 2112

Alfa AF: 0.455 Hom.: 1214

Bravo AF: 0.636

Asia WGS AF: 0.752 AC: 2611 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.64
DANN	Benign	0.33
PhyloP100		-0.15

Splicing

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

Other links and lift over

dbSNP: rs898939; hg19: chr14-84666749;