rs113317269

chr14-44577426-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 0.0397 in 152,246 control chromosomes in the GnomAD database, including 170 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 0.040 (170 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.738

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0658 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0397 AC: 6038 AN: 152128 Hom.: 170 Cov.: 33

Gnomad AFR AF: 0.0678

Gnomad AMI AF: 0.0923

Gnomad AMR AF: 0.0260

Gnomad ASJ AF: 0.0202

Gnomad EAS AF: 0.00365

Gnomad SAS AF: 0.0396

Gnomad FIN AF: 0.0334

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.0300

Gnomad OTH AF: 0.0335

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

GnomAD4 genome AF: 0.0397 AC: 6048 AN: 152246 Hom.: 170 Cov.: 33 AF XY: 0.0394 AC XY: 2930 AN XY: 74438

Gnomad4 AFR AF: 0.0679

Gnomad4 AMR AF: 0.0260

Gnomad4 ASJ AF: 0.0202

Gnomad4 EAS AF: 0.00347

Gnomad4 SAS AF: 0.0394

Gnomad4 FIN AF: 0.0334

Gnomad4 NFE AF: 0.0300

Gnomad4 OTH AF: 0.0332

Alfa AF: 0.0350 Hom.: 15

Bravo AF: 0.0395

Asia WGS AF: 0.0360 AC: 125 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	0.053
Dann	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs113317269; hg19: chr14-45046629;