14-95545726-A-T

Variant names:

• chr14-95545726-A-T
• rs10484055

Variant summary

Our verdict is Benign. The variant received -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: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.933
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	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

African (AFR) AF: 0.110 AC: 4583 AN: 41552

American (AMR) AF: 0.167 AC: 2562 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.00634 AC: 22 AN: 3470

East Asian (EAS) AF: 0.0447 AC: 231 AN: 5166

South Asian (SAS) AF: 0.0104 AC: 50 AN: 4828

European-Finnish (FIN) AF: 0.00961 AC: 102 AN: 10610

Middle Eastern (MID) AF: 0.00680 AC: 2 AN: 294

European-Non Finnish (NFE) AF: 0.00692 AC: 471 AN: 68030

Other (OTH) AF: 0.0492 AC: 104 AN: 2114

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.10
DANN	Benign	0.78
PhyloP100		-0.93

Splicing

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

Other links and lift over

dbSNP: rs10484055; hg19: chr14-96012063;