14-23686158-G-A

Variant names:

• chr14-23686158-G-A
• rs7141385

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 0.248 in 152,030 control chromosomes in the GnomAD database, including 5,540 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 0.25 (5540 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.555
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.54).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.507 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.247 AC: 37586 AN: 151912 Hom.: 5528 Cov.: 31

Gnomad AFR AF: 0.348

Gnomad AMI AF: 0.0680

Gnomad AMR AF: 0.308

Gnomad ASJ AF: 0.179

Gnomad EAS AF: 0.524

Gnomad SAS AF: 0.321

Gnomad FIN AF: 0.138

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.171

Gnomad OTH AF: 0.227

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

GnomAD4 genome AF: 0.248 AC: 37641 AN: 152030 Hom.: 5540 Cov.: 31 AF XY: 0.252 AC XY: 18717 AN XY: 74316

African (AFR) AF: 0.348 AC: 14397 AN: 41424

American (AMR) AF: 0.309 AC: 4710 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.179 AC: 621 AN: 3472

East Asian (EAS) AF: 0.523 AC: 2705 AN: 5168

South Asian (SAS) AF: 0.321 AC: 1547 AN: 4814

European-Finnish (FIN) AF: 0.138 AC: 1456 AN: 10588

Middle Eastern (MID) AF: 0.167 AC: 49 AN: 294

European-Non Finnish (NFE) AF: 0.171 AC: 11603 AN: 67984

Other (OTH) AF: 0.232 AC: 491 AN: 2114

Alfa AF: 0.202 Hom.: 11383

Bravo AF: 0.263

Asia WGS AF: 0.429 AC: 1492 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.54
CADD	Benign	11
DANN	Benign	0.83
PhyloP100		0.56

Splicing

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

Other links and lift over

dbSNP: rs7141385; hg19: chr14-24155367;