14-23345360-C-T

Variant names:

• chr14-23345360-C-T
• rs4982753

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 0.233 in 152,080 control chromosomes in the GnomAD database, including 5,275 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 0.23 (5275 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.08
• Publications: 30 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.404 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: 0.234 AC: 35486 AN: 151962 Hom.: 5272 Cov.: 32

Gnomad AFR AF: 0.0592

Gnomad AMI AF: 0.342

Gnomad AMR AF: 0.397

Gnomad ASJ AF: 0.302

Gnomad EAS AF: 0.418

Gnomad SAS AF: 0.235

Gnomad FIN AF: 0.381

Gnomad MID AF: 0.275

Gnomad NFE AF: 0.261

Gnomad OTH AF: 0.241

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

GnomAD4 genome AF: 0.233 AC: 35491 AN: 152080 Hom.: 5275 Cov.: 32 AF XY: 0.245 AC XY: 18178 AN XY: 74342

African (AFR) AF: 0.0590 AC: 2450 AN: 41514

American (AMR) AF: 0.397 AC: 6072 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.302 AC: 1047 AN: 3464

East Asian (EAS) AF: 0.418 AC: 2166 AN: 5176

South Asian (SAS) AF: 0.235 AC: 1134 AN: 4820

European-Finnish (FIN) AF: 0.381 AC: 4025 AN: 10560

Middle Eastern (MID) AF: 0.276 AC: 81 AN: 294

European-Non Finnish (NFE) AF: 0.261 AC: 17701 AN: 67942

Other (OTH) AF: 0.238 AC: 503 AN: 2112

Alfa AF: 0.244 Hom.: 9752

Bravo AF: 0.233

Asia WGS AF: 0.262 AC: 913 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	8.8
DANN	Benign	0.59
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs4982753; hg19: chr14-23814569;