rs943912

chr14-54918609-C-G

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 0.18 in 152,056 control chromosomes in the GnomAD database, including 2,544 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 0.18 (2544 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.75

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.218 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: 0.180 AC: 27318 AN: 151936 Hom.: 2543 Cov.: 31

Gnomad AFR AF: 0.155

Gnomad AMI AF: 0.309

Gnomad AMR AF: 0.224

Gnomad ASJ AF: 0.133

Gnomad EAS AF: 0.139

Gnomad SAS AF: 0.122

Gnomad FIN AF: 0.241

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.183

Gnomad OTH AF: 0.189

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

GnomAD4 genome AF: 0.180 AC: 27339 AN: 152056 Hom.: 2544 Cov.: 31 AF XY: 0.181 AC XY: 13487 AN XY: 74324

Gnomad4 AFR AF: 0.155

Gnomad4 AMR AF: 0.224

Gnomad4 ASJ AF: 0.133

Gnomad4 EAS AF: 0.139

Gnomad4 SAS AF: 0.122

Gnomad4 FIN AF: 0.241

Gnomad4 NFE AF: 0.183

Gnomad4 OTH AF: 0.188

Alfa AF: 0.178 Hom.: 348

Bravo AF: 0.178

Asia WGS AF: 0.123 AC: 429 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	0.062
Dann	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs943912; hg19: chr14-55385327;