14-83407824-G-T

Variant names:

• chr14-83407824-G-T
• rs229844

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 0.992 in 149,860 control chromosomes in the GnomAD database, including 73,780 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 0.99 (73780 hom., cov: 27)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.987 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: 0.992 AC: 148629 AN: 149780 Hom.: 73743 Cov.: 27

Gnomad AFR AF: 0.985

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.997

Gnomad ASJ AF: 0.996

Gnomad EAS AF: 0.998

Gnomad SAS AF: 0.997

Gnomad FIN AF: 0.998

Gnomad MID AF: 0.997

Gnomad NFE AF: 0.994

Gnomad OTH AF: 0.996

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

GnomAD4 genome AF: 0.992 AC: 148706 AN: 149860 Hom.: 73780 Cov.: 27 AF XY: 0.993 AC XY: 72593 AN XY: 73102

African (AFR) AF: 0.985 AC: 40179 AN: 40782

American (AMR) AF: 0.997 AC: 14984 AN: 15036

Ashkenazi Jewish (ASJ) AF: 0.996 AC: 3451 AN: 3466

East Asian (EAS) AF: 0.998 AC: 5066 AN: 5078

South Asian (SAS) AF: 0.997 AC: 4762 AN: 4776

European-Finnish (FIN) AF: 0.998 AC: 9931 AN: 9950

Middle Eastern (MID) AF: 0.997 AC: 289 AN: 290

European-Non Finnish (NFE) AF: 0.994 AC: 67054 AN: 67484

Other (OTH) AF: 0.996 AC: 2080 AN: 2088

Alfa AF: 0.994 Hom.: 14243

Bravo AF: 0.992

Asia WGS AF: 0.990 AC: 3434 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.98
DANN	Benign	0.30
PhyloP100		0.0

Splicing

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

Other links and lift over

dbSNP: rs229844; hg19: chr14-83874168;