rs10143866

Variant names:

• chr14-52417637-T-C
• rs10143866

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 0.25 in 152,026 control chromosomes in the GnomAD database, including 8,861 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 0.25 (8861 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.21

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.616 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: 0.250 AC: 37955 AN: 151908 Hom.: 8831 Cov.: 31

Gnomad AFR AF: 0.622

Gnomad AMI AF: 0.109

Gnomad AMR AF: 0.194

Gnomad ASJ AF: 0.102

Gnomad EAS AF: 0.0859

Gnomad SAS AF: 0.0801

Gnomad FIN AF: 0.0514

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.103

Gnomad OTH AF: 0.219

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

GnomAD4 genome AF: 0.250 AC: 38044 AN: 152026 Hom.: 8861 Cov.: 31 AF XY: 0.242 AC XY: 17964 AN XY: 74350

Gnomad4 AFR AF: 0.622

Gnomad4 AMR AF: 0.194

Gnomad4 ASJ AF: 0.102

Gnomad4 EAS AF: 0.0861

Gnomad4 SAS AF: 0.0800

Gnomad4 FIN AF: 0.0514

Gnomad4 NFE AF: 0.103

Gnomad4 OTH AF: 0.217

Alfa AF: 0.128 Hom.: 4191

Bravo AF: 0.279

Asia WGS AF: 0.138 AC: 480 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.98
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10143866; hg19: chr14-52884355;