14-44700086-C-T

Position:

• chr14-44700086-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 0.758 in 152,062 control chromosomes in the GnomAD database, including 44,249 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 0.76 (44249 hom., cov: 31)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.773

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.909 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.44700086C>T		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.758 AC: 115237 AN: 151944 Hom.: 44205 Cov.: 31

Gnomad AFR AF: 0.807

Gnomad AMI AF: 0.651

Gnomad AMR AF: 0.837

Gnomad ASJ AF: 0.784

Gnomad EAS AF: 0.931

Gnomad SAS AF: 0.815

Gnomad FIN AF: 0.575

Gnomad MID AF: 0.769

Gnomad NFE AF: 0.722

Gnomad OTH AF: 0.775

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

GnomAD4 genome AF: 0.758 AC: 115337 AN: 152062 Hom.: 44249 Cov.: 31 AF XY: 0.754 AC XY: 56071 AN XY: 74328

Gnomad4 AFR AF: 0.807

Gnomad4 AMR AF: 0.838

Gnomad4 ASJ AF: 0.784

Gnomad4 EAS AF: 0.931

Gnomad4 SAS AF: 0.816

Gnomad4 FIN AF: 0.575

Gnomad4 NFE AF: 0.722

Gnomad4 OTH AF: 0.778

Alfa AF: 0.739 Hom.: 21173

Bravo AF: 0.782

Asia WGS AF: 0.885 AC: 3078 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.35
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: rs807331; hg19: chr14-45169289;