14-23370824-C-T

Variant names:

• chr14-23370824-C-T
• rs10137082

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 0.225 in 152,118 control chromosomes in the GnomAD database, including 4,041 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 0.22 (4041 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.346
• Publications: 28 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 (AFR) allele frequency at 95% confidence interval = 0.24 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: 0.225 AC: 34180 AN: 152000 Hom.: 4029 Cov.: 32

Gnomad AFR AF: 0.244

Gnomad AMI AF: 0.139

Gnomad AMR AF: 0.207

Gnomad ASJ AF: 0.266

Gnomad EAS AF: 0.145

Gnomad SAS AF: 0.104

Gnomad FIN AF: 0.170

Gnomad MID AF: 0.250

Gnomad NFE AF: 0.238

Gnomad OTH AF: 0.255

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

GnomAD4 genome AF: 0.225 AC: 34217 AN: 152118 Hom.: 4041 Cov.: 32 AF XY: 0.219 AC XY: 16295 AN XY: 74386

African (AFR) AF: 0.244 AC: 10139 AN: 41482

American (AMR) AF: 0.206 AC: 3153 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.266 AC: 921 AN: 3466

East Asian (EAS) AF: 0.145 AC: 752 AN: 5178

South Asian (SAS) AF: 0.105 AC: 505 AN: 4824

European-Finnish (FIN) AF: 0.170 AC: 1795 AN: 10590

Middle Eastern (MID) AF: 0.238 AC: 70 AN: 294

European-Non Finnish (NFE) AF: 0.238 AC: 16211 AN: 67976

Other (OTH) AF: 0.258 AC: 544 AN: 2110

Alfa AF: 0.234 Hom.: 17755

Bravo AF: 0.232

Asia WGS AF: 0.153 AC: 532 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	3.1
DANN	Benign	0.45
PhyloP100		-0.35

Splicing

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

Other links and lift over

dbSNP: rs10137082; hg19: chr14-23840033;