chr14-88945090-A-T

Variant names:

• chr14-88945090-A-T
• rs41463644

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 0.26 in 152,056 control chromosomes in the GnomAD database, including 5,431 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 0.26 (5431 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.537
• 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 (NFE) allele frequency at 95% confidence interval = 0.307 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.260 AC: 39461 AN: 151938 Hom.: 5424 Cov.: 32

Gnomad AFR AF: 0.194

Gnomad AMI AF: 0.224

Gnomad AMR AF: 0.235

Gnomad ASJ AF: 0.342

Gnomad EAS AF: 0.231

Gnomad SAS AF: 0.211

Gnomad FIN AF: 0.228

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.310

Gnomad OTH AF: 0.292

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

GnomAD4 genome AF: 0.260 AC: 39483 AN: 152056 Hom.: 5431 Cov.: 32 AF XY: 0.256 AC XY: 19063 AN XY: 74352

African (AFR) AF: 0.194 AC: 8058 AN: 41474

American (AMR) AF: 0.235 AC: 3583 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.342 AC: 1185 AN: 3468

East Asian (EAS) AF: 0.231 AC: 1194 AN: 5164

South Asian (SAS) AF: 0.211 AC: 1015 AN: 4820

European-Finnish (FIN) AF: 0.228 AC: 2417 AN: 10590

Middle Eastern (MID) AF: 0.391 AC: 115 AN: 294

European-Non Finnish (NFE) AF: 0.310 AC: 21090 AN: 67954

Other (OTH) AF: 0.295 AC: 622 AN: 2110

Alfa AF: 0.279 Hom.: 773

Bravo AF: 0.257

Asia WGS AF: 0.233 AC: 811 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	1.2
DANN	Benign	0.73
PhyloP100		-0.54

Splicing

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

Other links and lift over

dbSNP: rs41463644; hg19: chr14-89411434;