chr14-101223708-G-T

Variant names:

• chr14-101223708-G-T
• rs8008758

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 0.271 in 152,112 control chromosomes in the GnomAD database, including 5,907 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 0.27 (5907 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.328
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.297 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: 0.271 AC: 41249 AN: 151994 Hom.: 5912 Cov.: 33

Gnomad AFR AF: 0.253

Gnomad AMI AF: 0.264

Gnomad AMR AF: 0.287

Gnomad ASJ AF: 0.222

Gnomad EAS AF: 0.104

Gnomad SAS AF: 0.136

Gnomad FIN AF: 0.290

Gnomad MID AF: 0.316

Gnomad NFE AF: 0.300

Gnomad OTH AF: 0.291

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

GnomAD4 genome AF: 0.271 AC: 41272 AN: 152112 Hom.: 5907 Cov.: 33 AF XY: 0.267 AC XY: 19835 AN XY: 74358

African (AFR) AF: 0.253 AC: 10497 AN: 41498

American (AMR) AF: 0.288 AC: 4400 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.222 AC: 770 AN: 3470

East Asian (EAS) AF: 0.104 AC: 539 AN: 5182

South Asian (SAS) AF: 0.135 AC: 650 AN: 4826

European-Finnish (FIN) AF: 0.290 AC: 3065 AN: 10556

Middle Eastern (MID) AF: 0.337 AC: 99 AN: 294

European-Non Finnish (NFE) AF: 0.300 AC: 20400 AN: 67976

Other (OTH) AF: 0.290 AC: 611 AN: 2110

Alfa AF: 0.287 Hom.: 9532

Bravo AF: 0.276

Asia WGS AF: 0.156 AC: 544 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	3.5
DANN	Benign	0.88
PhyloP100		0.33

Splicing

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

Other links and lift over

dbSNP: rs8008758; hg19: chr14-101690045;