14-20414432-T-C

Variant names:

• chr14-20414432-T-C
• rs4246977

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 0.359 in 152,068 control chromosomes in the GnomAD database, including 9,971 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 0.36 (9971 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.391

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.429 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: 0.359 AC: 54482 AN: 151952 Hom.: 9955 Cov.: 32

Gnomad AFR AF: 0.298

Gnomad AMI AF: 0.397

Gnomad AMR AF: 0.329

Gnomad ASJ AF: 0.368

Gnomad EAS AF: 0.305

Gnomad SAS AF: 0.444

Gnomad FIN AF: 0.379

Gnomad MID AF: 0.456

Gnomad NFE AF: 0.395

Gnomad OTH AF: 0.363

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

GnomAD4 genome AF: 0.359 AC: 54538 AN: 152068 Hom.: 9971 Cov.: 32 AF XY: 0.360 AC XY: 26784 AN XY: 74360

Gnomad4 AFR AF: 0.298

Gnomad4 AMR AF: 0.329

Gnomad4 ASJ AF: 0.368

Gnomad4 EAS AF: 0.306

Gnomad4 SAS AF: 0.445

Gnomad4 FIN AF: 0.379

Gnomad4 NFE AF: 0.395

Gnomad4 OTH AF: 0.366

Alfa AF: 0.386 Hom.: 19203

Bravo AF: 0.349

Asia WGS AF: 0.319 AC: 1109 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.2
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4246977; hg19: chr14-20882591;