rs11624776

chr14-93129246-A-Cchr14-93129246-A-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 0.259 in 152,190 control chromosomes in the GnomAD database, including 5,896 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 (5896 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.614

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.337 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: 0.259 AC: 39434 AN: 152072 Hom.: 5890 Cov.: 33

Gnomad AFR AF: 0.105

Gnomad AMI AF: 0.350

Gnomad AMR AF: 0.345

Gnomad ASJ AF: 0.339

Gnomad EAS AF: 0.157

Gnomad SAS AF: 0.304

Gnomad FIN AF: 0.312

Gnomad MID AF: 0.291

Gnomad NFE AF: 0.325

Gnomad OTH AF: 0.290

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

GnomAD4 genome AF: 0.259 AC: 39449 AN: 152190 Hom.: 5896 Cov.: 33 AF XY: 0.262 AC XY: 19503 AN XY: 74406

Gnomad4 AFR AF: 0.104

Gnomad4 AMR AF: 0.345

Gnomad4 ASJ AF: 0.339

Gnomad4 EAS AF: 0.157

Gnomad4 SAS AF: 0.304

Gnomad4 FIN AF: 0.312

Gnomad4 NFE AF: 0.325

Gnomad4 OTH AF: 0.293

Alfa AF: 0.237 Hom.: 1089

Bravo AF: 0.252

Asia WGS AF: 0.259 AC: 901 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
Cadd	Benign	14
Dann	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11624776; hg19: chr14-93595591;