chr14-106539448-C-T

Position:

• chr14-106539448-C-T

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 0.312 in 151,754 control chromosomes in the GnomAD database, including 8,600 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 0.31 (8600 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.138

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (Cadd=5.209).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.399 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: 0.312 AC: 47347 AN: 151644 Hom.: 8603 Cov.: 33

Gnomad AFR AF: 0.120

Gnomad AMI AF: 0.403

Gnomad AMR AF: 0.407

Gnomad ASJ AF: 0.320

Gnomad EAS AF: 0.402

Gnomad SAS AF: 0.256

Gnomad FIN AF: 0.368

Gnomad MID AF: 0.329

Gnomad NFE AF: 0.394

Gnomad OTH AF: 0.341

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

GnomAD4 genome AF: 0.312 AC: 47350 AN: 151754 Hom.: 8600 Cov.: 33 AF XY: 0.310 AC XY: 22992 AN XY: 74178

Gnomad4 AFR AF: 0.120

Gnomad4 AMR AF: 0.407

Gnomad4 ASJ AF: 0.320

Gnomad4 EAS AF: 0.402

Gnomad4 SAS AF: 0.258

Gnomad4 FIN AF: 0.368

Gnomad4 NFE AF: 0.393

Gnomad4 OTH AF: 0.340

Alfa AF: 0.334 Hom.: 1155

Bravo AF: 0.308

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
CADD	Benign	5.2

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10151262; hg19: -;