rs1471547

Variant names:

• chr14-55971649-C-T
• rs1471547

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 0.331 in 152,030 control chromosomes in the GnomAD database, including 10,258 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 0.33 (10258 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.584

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.44 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: 0.331 AC: 50325 AN: 151912 Hom.: 10256 Cov.: 32

Gnomad AFR AF: 0.0848

Gnomad AMI AF: 0.457

Gnomad AMR AF: 0.366

Gnomad ASJ AF: 0.457

Gnomad EAS AF: 0.452

Gnomad SAS AF: 0.293

Gnomad FIN AF: 0.411

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.445

Gnomad OTH AF: 0.378

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

GnomAD4 genome AF: 0.331 AC: 50326 AN: 152030 Hom.: 10258 Cov.: 32 AF XY: 0.331 AC XY: 24578 AN XY: 74296

Gnomad4 AFR AF: 0.0846

Gnomad4 AMR AF: 0.366

Gnomad4 ASJ AF: 0.457

Gnomad4 EAS AF: 0.453

Gnomad4 SAS AF: 0.294

Gnomad4 FIN AF: 0.411

Gnomad4 NFE AF: 0.445

Gnomad4 OTH AF: 0.374

Alfa AF: 0.405 Hom.: 6738

Bravo AF: 0.322

Asia WGS AF: 0.314 AC: 1091 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.8
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1471547; hg19: chr14-56438367;