14-97996820-T-C

Position:

• chr14-97996820-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 0.37 in 151,992 control chromosomes in the GnomAD database, including 13,388 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 0.37 (13388 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.72

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 (AFR) allele frequency at 95% confidence interval = 0.656 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: 0.370 AC: 56130 AN: 151874 Hom.: 13348 Cov.: 32

Gnomad AFR AF: 0.662

Gnomad AMI AF: 0.137

Gnomad AMR AF: 0.311

Gnomad ASJ AF: 0.207

Gnomad EAS AF: 0.534

Gnomad SAS AF: 0.440

Gnomad FIN AF: 0.329

Gnomad MID AF: 0.245

Gnomad NFE AF: 0.207

Gnomad OTH AF: 0.330

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

GnomAD4 genome AF: 0.370 AC: 56231 AN: 151992 Hom.: 13388 Cov.: 32 AF XY: 0.378 AC XY: 28046 AN XY: 74266

Gnomad4 AFR AF: 0.662

Gnomad4 AMR AF: 0.311

Gnomad4 ASJ AF: 0.207

Gnomad4 EAS AF: 0.534

Gnomad4 SAS AF: 0.441

Gnomad4 FIN AF: 0.329

Gnomad4 NFE AF: 0.207

Gnomad4 OTH AF: 0.338

Alfa AF: 0.248 Hom.: 2367

Bravo AF: 0.377

Asia WGS AF: 0.518 AC: 1797 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	0.058
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7140601; hg19: chr14-98463157;