rs11624318

chr14-94839675-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 0.148 in 152,068 control chromosomes in the GnomAD database, including 2,187 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 0.15 (2187 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.488

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 = 0.202 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: 0.148 AC: 22507 AN: 151950 Hom.: 2185 Cov.: 32

Gnomad AFR AF: 0.0375

Gnomad AMI AF: 0.106

Gnomad AMR AF: 0.130

Gnomad ASJ AF: 0.140

Gnomad EAS AF: 0.127

Gnomad SAS AF: 0.107

Gnomad FIN AF: 0.282

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.205

Gnomad OTH AF: 0.134

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

GnomAD4 genome AF: 0.148 AC: 22512 AN: 152068 Hom.: 2187 Cov.: 32 AF XY: 0.150 AC XY: 11140 AN XY: 74316

Gnomad4 AFR AF: 0.0374

Gnomad4 AMR AF: 0.130

Gnomad4 ASJ AF: 0.140

Gnomad4 EAS AF: 0.128

Gnomad4 SAS AF: 0.108

Gnomad4 FIN AF: 0.282

Gnomad4 NFE AF: 0.205

Gnomad4 OTH AF: 0.133

Alfa AF: 0.188 Hom.: 3780

Bravo AF: 0.131

Asia WGS AF: 0.124 AC: 430 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	0.029
Dann	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11624318; hg19: chr14-95306012;