rs2753571

chr14-105786362-C-Achr14-105786362-C-Gchr14-105786362-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 0.41 in 149,292 control chromosomes in the GnomAD database, including 13,982 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 0.41 (13982 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.266

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.961 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: 0.410 AC: 61109 AN: 149188 Hom.: 13947 Cov.: 32

Gnomad AFR AF: 0.403

Gnomad AMI AF: 0.307

Gnomad AMR AF: 0.550

Gnomad ASJ AF: 0.242

Gnomad EAS AF: 0.984

Gnomad SAS AF: 0.558

Gnomad FIN AF: 0.444

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.339

Gnomad OTH AF: 0.407

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

GnomAD4 genome AF: 0.410 AC: 61190 AN: 149292 Hom.: 13982 Cov.: 32 AF XY: 0.425 AC XY: 30905 AN XY: 72770

Gnomad4 AFR AF: 0.403

Gnomad4 AMR AF: 0.551

Gnomad4 ASJ AF: 0.242

Gnomad4 EAS AF: 0.984

Gnomad4 SAS AF: 0.558

Gnomad4 FIN AF: 0.444

Gnomad4 NFE AF: 0.339

Gnomad4 OTH AF: 0.410

Alfa AF: 0.201 Hom.: 374

Bravo AF: 0.422

Asia WGS AF: 0.744 AC: 2549 AN: 3428

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	3.4
Dann	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2753571; hg19: chr14-106252699;