14-24341164-T-C

Position:

• chr14-24341164-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.2 in 152,132 control chromosomes in the GnomAD database, including 3,885 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 0.20 (3885 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0220

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.323 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.200 AC: 30418 AN: 152014 Hom.: 3873 Cov.: 33

Gnomad AFR AF: 0.0506

Gnomad AMI AF: 0.160

Gnomad AMR AF: 0.330

Gnomad ASJ AF: 0.163

Gnomad EAS AF: 0.243

Gnomad SAS AF: 0.254

Gnomad FIN AF: 0.205

Gnomad MID AF: 0.156

Gnomad NFE AF: 0.256

Gnomad OTH AF: 0.216

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

GnomAD4 genome AF: 0.200 AC: 30444 AN: 152132 Hom.: 3885 Cov.: 33 AF XY: 0.201 AC XY: 14924 AN XY: 74376

Gnomad4 AFR AF: 0.0504

Gnomad4 AMR AF: 0.330

Gnomad4 ASJ AF: 0.163

Gnomad4 EAS AF: 0.243

Gnomad4 SAS AF: 0.254

Gnomad4 FIN AF: 0.205

Gnomad4 NFE AF: 0.256

Gnomad4 OTH AF: 0.225

Alfa AF: 0.246 Hom.: 9814

Bravo AF: 0.204

Asia WGS AF: 0.259 AC: 900 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	9.5
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3212243; hg19: chr14-24810370;