14-86725072-A-T

Variant names:

• chr14-86725072-A-T
• rs2159645

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 0.429 in 152,008 control chromosomes in the GnomAD database, including 14,153 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 0.43 (14153 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.312

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.518 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.429 AC: 65147 AN: 151890 Hom.: 14135 Cov.: 32

Gnomad AFR AF: 0.360

Gnomad AMI AF: 0.425

Gnomad AMR AF: 0.469

Gnomad ASJ AF: 0.474

Gnomad EAS AF: 0.533

Gnomad SAS AF: 0.440

Gnomad FIN AF: 0.545

Gnomad MID AF: 0.358

Gnomad NFE AF: 0.434

Gnomad OTH AF: 0.421

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

GnomAD4 genome AF: 0.429 AC: 65197 AN: 152008 Hom.: 14153 Cov.: 32 AF XY: 0.436 AC XY: 32393 AN XY: 74302

Gnomad4 AFR AF: 0.360

Gnomad4 AMR AF: 0.469

Gnomad4 ASJ AF: 0.474

Gnomad4 EAS AF: 0.534

Gnomad4 SAS AF: 0.441

Gnomad4 FIN AF: 0.545

Gnomad4 NFE AF: 0.434

Gnomad4 OTH AF: 0.420

Alfa AF: 0.444 Hom.: 1885

Bravo AF: 0.415

Asia WGS AF: 0.416 AC: 1450 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	6.9
DANN	Benign	0.86

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2159645; hg19: chr14-87191416;