rs11625623

Variant names:

• chr14-52292628-A-G
• rs11625623

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 0.203 in 151,976 control chromosomes in the GnomAD database, including 3,245 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 0.20 (3245 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.129

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 (SAS) allele frequency at 95% confidence interval = 0.329 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: 0.203 AC: 30810 AN: 151858 Hom.: 3235 Cov.: 32

Gnomad AFR AF: 0.176

Gnomad AMI AF: 0.414

Gnomad AMR AF: 0.164

Gnomad ASJ AF: 0.242

Gnomad EAS AF: 0.137

Gnomad SAS AF: 0.341

Gnomad FIN AF: 0.168

Gnomad MID AF: 0.325

Gnomad NFE AF: 0.223

Gnomad OTH AF: 0.210

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

GnomAD4 genome AF: 0.203 AC: 30841 AN: 151976 Hom.: 3245 Cov.: 32 AF XY: 0.203 AC XY: 15121 AN XY: 74322

Gnomad4 AFR AF: 0.176

Gnomad4 AMR AF: 0.164

Gnomad4 ASJ AF: 0.242

Gnomad4 EAS AF: 0.138

Gnomad4 SAS AF: 0.343

Gnomad4 FIN AF: 0.168

Gnomad4 NFE AF: 0.223

Gnomad4 OTH AF: 0.210

Alfa AF: 0.216 Hom.: 454

Bravo AF: 0.198

Asia WGS AF: 0.213 AC: 730 AN: 3430

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	11
DANN	Benign	0.89

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11625623; hg19: chr14-52759346;