chr14-104798626-A-G

Variant names:

• chr14-104798626-A-G
• rs2498784

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 0.844 in 152,188 control chromosomes in the GnomAD database, including 55,385 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 0.84 (55385 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.112
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.917 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: 0.844 AC: 128399 AN: 152070 Hom.: 55341 Cov.: 33

Gnomad AFR AF: 0.796

Gnomad AMI AF: 0.936

Gnomad AMR AF: 0.784

Gnomad ASJ AF: 0.886

Gnomad EAS AF: 0.335

Gnomad SAS AF: 0.660

Gnomad FIN AF: 0.928

Gnomad MID AF: 0.801

Gnomad NFE AF: 0.923

Gnomad OTH AF: 0.849

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

GnomAD4 genome AF: 0.844 AC: 128508 AN: 152188 Hom.: 55385 Cov.: 33 AF XY: 0.837 AC XY: 62328 AN XY: 74422

African (AFR) AF: 0.796 AC: 32999 AN: 41468

American (AMR) AF: 0.784 AC: 11986 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.886 AC: 3075 AN: 3472

East Asian (EAS) AF: 0.337 AC: 1743 AN: 5178

South Asian (SAS) AF: 0.662 AC: 3193 AN: 4826

European-Finnish (FIN) AF: 0.928 AC: 9844 AN: 10610

Middle Eastern (MID) AF: 0.803 AC: 236 AN: 294

European-Non Finnish (NFE) AF: 0.923 AC: 62789 AN: 68018

Other (OTH) AF: 0.845 AC: 1789 AN: 2116

Alfa AF: 0.879 Hom.: 8920

Bravo AF: 0.832

Asia WGS AF: 0.515 AC: 1794 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.6
DANN	Benign	0.62
PhyloP100		-0.11

Splicing

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

Other links and lift over

dbSNP: rs2498784; hg19: chr14-105264963;