chr14-23808776-A-C

Variant names:

• chr14-23808776-A-C
• rs1952415

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 0.343 in 151,896 control chromosomes in the GnomAD database, including 9,506 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 0.34 (9506 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.437
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.467 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: 0.343 AC: 52102 AN: 151778 Hom.: 9495 Cov.: 32

Gnomad AFR AF: 0.471

Gnomad AMI AF: 0.519

Gnomad AMR AF: 0.278

Gnomad ASJ AF: 0.272

Gnomad EAS AF: 0.482

Gnomad SAS AF: 0.352

Gnomad FIN AF: 0.329

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.274

Gnomad OTH AF: 0.314

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

GnomAD4 genome AF: 0.343 AC: 52167 AN: 151896 Hom.: 9506 Cov.: 32 AF XY: 0.348 AC XY: 25818 AN XY: 74248

African (AFR) AF: 0.472 AC: 19513 AN: 41376

American (AMR) AF: 0.277 AC: 4230 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.272 AC: 943 AN: 3464

East Asian (EAS) AF: 0.483 AC: 2494 AN: 5166

South Asian (SAS) AF: 0.353 AC: 1698 AN: 4804

European-Finnish (FIN) AF: 0.329 AC: 3467 AN: 10550

Middle Eastern (MID) AF: 0.207 AC: 61 AN: 294

European-Non Finnish (NFE) AF: 0.274 AC: 18629 AN: 67964

Other (OTH) AF: 0.313 AC: 660 AN: 2110

Alfa AF: 0.292 Hom.: 28959

Bravo AF: 0.343

Asia WGS AF: 0.436 AC: 1511 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.5
DANN	Benign	0.48
PhyloP100		-0.44

Splicing

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

Other links and lift over

dbSNP: rs1952415; hg19: chr14-24277985;