chr14-53948573-C-T

Position:

• chr14-53948573-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 0.359 in 151,554 control chromosomes in the GnomAD database, including 10,238 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 (10231 hom., cov: 28)
  • Exomes 𝑓: 0.52 (7 hom.)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.614

Genes affected

(HGNC:):

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 = 0.459 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.53948573C>T		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.359 AC: 54368 AN: 151382 Hom.: 10235 Cov.: 28

Gnomad AFR AF: 0.235

Gnomad AMI AF: 0.434

Gnomad AMR AF: 0.424

Gnomad ASJ AF: 0.460

Gnomad EAS AF: 0.419

Gnomad SAS AF: 0.475

Gnomad FIN AF: 0.345

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.402

Gnomad OTH AF: 0.389

GnomAD4 exome AF: 0.519 AC: 28 AN: 54 Hom.: 7 AF XY: 0.607 AC XY: 17 AN XY: 28

Gnomad4 AFR exome AF: 0.500

Gnomad4 EAS exome AF: 0.00

Gnomad4 NFE exome AF: 0.667

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.359 AC: 54380 AN: 151500 Hom.: 10231 Cov.: 28 AF XY: 0.362 AC XY: 26776 AN XY: 74004

Gnomad4 AFR AF: 0.235

Gnomad4 AMR AF: 0.423

Gnomad4 ASJ AF: 0.460

Gnomad4 EAS AF: 0.420

Gnomad4 SAS AF: 0.475

Gnomad4 FIN AF: 0.345

Gnomad4 NFE AF: 0.402

Gnomad4 OTH AF: 0.390

Alfa AF: 0.394 Hom.: 5058

Bravo AF: 0.357

Asia WGS AF: 0.448 AC: 1561 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	0.80
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12898159; hg19: chr14-54415291;