14-23814964-A-G

Variant names:

• chr14-23814964-A-G
• rs12100601

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 0.173 in 152,156 control chromosomes in the GnomAD database, including 2,367 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 0.17 (2367 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.03
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.198 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: 0.173 AC: 26340 AN: 152038 Hom.: 2368 Cov.: 32

Gnomad AFR AF: 0.143

Gnomad AMI AF: 0.307

Gnomad AMR AF: 0.146

Gnomad ASJ AF: 0.174

Gnomad EAS AF: 0.0831

Gnomad SAS AF: 0.137

Gnomad FIN AF: 0.207

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.201

Gnomad OTH AF: 0.164

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

GnomAD4 genome AF: 0.173 AC: 26349 AN: 152156 Hom.: 2367 Cov.: 32 AF XY: 0.173 AC XY: 12905 AN XY: 74384

African (AFR) AF: 0.143 AC: 5930 AN: 41496

American (AMR) AF: 0.146 AC: 2230 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.174 AC: 605 AN: 3468

East Asian (EAS) AF: 0.0829 AC: 430 AN: 5188

South Asian (SAS) AF: 0.138 AC: 665 AN: 4822

European-Finnish (FIN) AF: 0.207 AC: 2193 AN: 10574

Middle Eastern (MID) AF: 0.0884 AC: 26 AN: 294

European-Non Finnish (NFE) AF: 0.201 AC: 13648 AN: 67992

Other (OTH) AF: 0.162 AC: 342 AN: 2112

Alfa AF: 0.115 Hom.: 232

Bravo AF: 0.169

Asia WGS AF: 0.114 AC: 397 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	11
DANN	Benign	0.74
PhyloP100		1.0

Splicing

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

Other links and lift over

dbSNP: rs12100601; hg19: chr14-24284173;