rs1243575

Positions:

• chr14-94914865-C-A

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 0.257 in 152,216 control chromosomes in the GnomAD database, including 6,458 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 0.26 (6458 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.689

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.36 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.257 AC: 39120 AN: 152098 Hom.: 6454 Cov.: 33

Gnomad AFR AF: 0.0677

Gnomad AMI AF: 0.395

Gnomad AMR AF: 0.237

Gnomad ASJ AF: 0.377

Gnomad EAS AF: 0.130

Gnomad SAS AF: 0.177

Gnomad FIN AF: 0.386

Gnomad MID AF: 0.294

Gnomad NFE AF: 0.364

Gnomad OTH AF: 0.285

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

GnomAD4 genome AF: 0.257 AC: 39135 AN: 152216 Hom.: 6458 Cov.: 33 AF XY: 0.257 AC XY: 19100 AN XY: 74394

Gnomad4 AFR AF: 0.0676

Gnomad4 AMR AF: 0.237

Gnomad4 ASJ AF: 0.377

Gnomad4 EAS AF: 0.130

Gnomad4 SAS AF: 0.178

Gnomad4 FIN AF: 0.386

Gnomad4 NFE AF: 0.364

Gnomad4 OTH AF: 0.288

Alfa AF: 0.304 Hom.: 995

Bravo AF: 0.240

Asia WGS AF: 0.140 AC: 491 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.63
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1243575; hg19: chr14-95381202;