rs11627027

Variant names:

• chr14-93904071-C-T
• rs11627027

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 0.195 in 152,188 control chromosomes in the GnomAD database, including 3,790 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 0.19 (3790 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0430

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.274 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: 0.195 AC: 29667 AN: 152070 Hom.: 3792 Cov.: 33

Gnomad AFR AF: 0.0605

Gnomad AMI AF: 0.489

Gnomad AMR AF: 0.175

Gnomad ASJ AF: 0.310

Gnomad EAS AF: 0.00308

Gnomad SAS AF: 0.137

Gnomad FIN AF: 0.276

Gnomad MID AF: 0.264

Gnomad NFE AF: 0.277

Gnomad OTH AF: 0.216

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

GnomAD4 genome AF: 0.195 AC: 29663 AN: 152188 Hom.: 3790 Cov.: 33 AF XY: 0.194 AC XY: 14426 AN XY: 74400

Gnomad4 AFR AF: 0.0603

Gnomad4 AMR AF: 0.175

Gnomad4 ASJ AF: 0.310

Gnomad4 EAS AF: 0.00309

Gnomad4 SAS AF: 0.137

Gnomad4 FIN AF: 0.276

Gnomad4 NFE AF: 0.277

Gnomad4 OTH AF: 0.214

Alfa AF: 0.250 Hom.: 1293

Bravo AF: 0.182

Asia WGS AF: 0.0620 AC: 217 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	4.3
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11627027; hg19: chr14-94370417;