chr14-66313845-C-T

Position:

• chr14-66313845-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 0.273 in 152,022 control chromosomes in the GnomAD database, including 7,498 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 0.27 (7498 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.135

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.464 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.66313845C>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000258561	ENST00000556361.1	n.65-64611G>A		intron_variant		3
ENSG00000258561	ENST00000556874.1	n.644-82950G>A		intron_variant		2
ENSG00000258561	ENST00000654014.1	n.370-44803G>A		intron_variant

Frequencies

GnomAD3 genomes AF: 0.273 AC: 41401 AN: 151904 Hom.: 7458 Cov.: 32

Gnomad AFR AF: 0.469

Gnomad AMI AF: 0.249

Gnomad AMR AF: 0.362

Gnomad ASJ AF: 0.221

Gnomad EAS AF: 0.478

Gnomad SAS AF: 0.317

Gnomad FIN AF: 0.150

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.137

Gnomad OTH AF: 0.275

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

GnomAD4 genome AF: 0.273 AC: 41505 AN: 152022 Hom.: 7498 Cov.: 32 AF XY: 0.278 AC XY: 20699 AN XY: 74324

Gnomad4 AFR AF: 0.469

Gnomad4 AMR AF: 0.362

Gnomad4 ASJ AF: 0.221

Gnomad4 EAS AF: 0.478

Gnomad4 SAS AF: 0.318

Gnomad4 FIN AF: 0.150

Gnomad4 NFE AF: 0.136

Gnomad4 OTH AF: 0.279

Alfa AF: 0.168 Hom.: 4452

Bravo AF: 0.298

Asia WGS AF: 0.401 AC: 1396 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	3.2
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2053149; hg19: chr14-66780563;