14-104796624-G-A

Variant names:

• chr14-104796624-G-A
• rs2494751

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 0.842 in 152,238 control chromosomes in the GnomAD database, including 55,124 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 (55124 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.960
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.72).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.916 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: 0.842 AC: 128104 AN: 152120 Hom.: 55082 Cov.: 34

Gnomad AFR AF: 0.791

Gnomad AMI AF: 0.936

Gnomad AMR AF: 0.781

Gnomad ASJ AF: 0.880

Gnomad EAS AF: 0.334

Gnomad SAS AF: 0.657

Gnomad FIN AF: 0.928

Gnomad MID AF: 0.799

Gnomad NFE AF: 0.922

Gnomad OTH AF: 0.847

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

GnomAD4 genome AF: 0.842 AC: 128212 AN: 152238 Hom.: 55124 Cov.: 34 AF XY: 0.836 AC XY: 62182 AN XY: 74424

African (AFR) AF: 0.791 AC: 32833 AN: 41492

American (AMR) AF: 0.781 AC: 11963 AN: 15312

Ashkenazi Jewish (ASJ) AF: 0.880 AC: 3055 AN: 3472

East Asian (EAS) AF: 0.335 AC: 1736 AN: 5180

South Asian (SAS) AF: 0.659 AC: 3178 AN: 4820

European-Finnish (FIN) AF: 0.928 AC: 9847 AN: 10614

Middle Eastern (MID) AF: 0.801 AC: 234 AN: 292

European-Non Finnish (NFE) AF: 0.922 AC: 62729 AN: 68032

Other (OTH) AF: 0.844 AC: 1783 AN: 2112

Alfa AF: 0.883 Hom.: 7596

Bravo AF: 0.830

Asia WGS AF: 0.513 AC: 1787 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	1.8
DANN	Benign	0.88
PhyloP100		-0.96

Splicing

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

Other links and lift over

dbSNP: rs2494751; hg19: chr14-105262961;