14-99682624-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 0.673 in 151,980 control chromosomes in the GnomAD database, including 35,327 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 0.67 (35327 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.39

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.815 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.673 AC: 102202 AN: 151862 Hom.: 35321 Cov.: 31

Gnomad AFR AF: 0.513

Gnomad AMI AF: 0.808

Gnomad AMR AF: 0.687

Gnomad ASJ AF: 0.719

Gnomad EAS AF: 0.601

Gnomad SAS AF: 0.837

Gnomad FIN AF: 0.739

Gnomad MID AF: 0.747

Gnomad NFE AF: 0.746

Gnomad OTH AF: 0.676

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

GnomAD4 genome AF: 0.673 AC: 102247 AN: 151980 Hom.: 35327 Cov.: 31 AF XY: 0.676 AC XY: 50250 AN XY: 74282

Gnomad4 AFR AF: 0.513

Gnomad4 AMR AF: 0.686

Gnomad4 ASJ AF: 0.719

Gnomad4 EAS AF: 0.601

Gnomad4 SAS AF: 0.836

Gnomad4 FIN AF: 0.739

Gnomad4 NFE AF: 0.746

Gnomad4 OTH AF: 0.675

Alfa AF: 0.710 Hom.: 8032

Bravo AF: 0.659

Asia WGS AF: 0.710 AC: 2470 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	2.1
Dann	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8003602; hg19: chr14-100148961;