14-95545726-A-T

Position:

• chr14-95545726-A-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 0.0534 in 152,282 control chromosomes in the GnomAD database, including 534 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 0.053 (534 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.933

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.162 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.95545726A>T		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0532 AC: 8099 AN: 152164 Hom.: 529 Cov.: 32

Gnomad AFR AF: 0.110

Gnomad AMI AF: 0.00658

Gnomad AMR AF: 0.167

Gnomad ASJ AF: 0.00634

Gnomad EAS AF: 0.0446

Gnomad SAS AF: 0.0101

Gnomad FIN AF: 0.00961

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.00692

Gnomad OTH AF: 0.0497

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

GnomAD4 genome AF: 0.0534 AC: 8133 AN: 152282 Hom.: 534 Cov.: 32 AF XY: 0.0559 AC XY: 4165 AN XY: 74450

Gnomad4 AFR AF: 0.110

Gnomad4 AMR AF: 0.167

Gnomad4 ASJ AF: 0.00634

Gnomad4 EAS AF: 0.0447

Gnomad4 SAS AF: 0.0104

Gnomad4 FIN AF: 0.00961

Gnomad4 NFE AF: 0.00692

Gnomad4 OTH AF: 0.0492

Alfa AF: 0.00336 Hom.: 0

Bravo AF: 0.0682

Asia WGS AF: 0.0520 AC: 181 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.10
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10484055; hg19: chr14-96012063;