chr14-98628946-T-G

Variant names:

• chr14-98628946-T-G
• rs926949

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 152,180 control chromosomes in the GnomAD database, including 54,213 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 (54213 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.691
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.969 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.842 AC: 128001 AN: 152062 Hom.: 54147 Cov.: 33

Gnomad AFR AF: 0.905

Gnomad AMI AF: 0.865

Gnomad AMR AF: 0.842

Gnomad ASJ AF: 0.795

Gnomad EAS AF: 0.991

Gnomad SAS AF: 0.922

Gnomad FIN AF: 0.809

Gnomad MID AF: 0.737

Gnomad NFE AF: 0.795

Gnomad OTH AF: 0.816

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

GnomAD4 genome AF: 0.842 AC: 128127 AN: 152180 Hom.: 54213 Cov.: 33 AF XY: 0.845 AC XY: 62888 AN XY: 74394

African (AFR) AF: 0.905 AC: 37587 AN: 41542

American (AMR) AF: 0.842 AC: 12871 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.795 AC: 2760 AN: 3470

East Asian (EAS) AF: 0.991 AC: 5117 AN: 5162

South Asian (SAS) AF: 0.922 AC: 4448 AN: 4824

European-Finnish (FIN) AF: 0.809 AC: 8577 AN: 10600

Middle Eastern (MID) AF: 0.741 AC: 218 AN: 294

European-Non Finnish (NFE) AF: 0.795 AC: 54031 AN: 67984

Other (OTH) AF: 0.818 AC: 1731 AN: 2116

Alfa AF: 0.837 Hom.: 9292

Bravo AF: 0.845

Asia WGS AF: 0.949 AC: 3299 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	9.8
DANN	Benign	0.71
PhyloP100		0.69

Splicing

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

Other links and lift over

dbSNP: rs926949; hg19: chr14-99095283;