rs11621151

chr14-28554895-C-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 0.0815 in 152,062 control chromosomes in the GnomAD database, including 744 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 0.082 (744 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.307

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.204 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: 0.0814 AC: 12363 AN: 151942 Hom.: 735 Cov.: 32

Gnomad AFR AF: 0.0470

Gnomad AMI AF: 0.124

Gnomad AMR AF: 0.208

Gnomad ASJ AF: 0.129

Gnomad EAS AF: 0.0313

Gnomad SAS AF: 0.0408

Gnomad FIN AF: 0.0721

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.0791

Gnomad OTH AF: 0.0761

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

GnomAD4 genome AF: 0.0815 AC: 12396 AN: 152062 Hom.: 744 Cov.: 32 AF XY: 0.0824 AC XY: 6125 AN XY: 74324

Gnomad4 AFR AF: 0.0470

Gnomad4 AMR AF: 0.210

Gnomad4 ASJ AF: 0.129

Gnomad4 EAS AF: 0.0314

Gnomad4 SAS AF: 0.0414

Gnomad4 FIN AF: 0.0721

Gnomad4 NFE AF: 0.0791

Gnomad4 OTH AF: 0.0753

Alfa AF: 0.0841 Hom.: 929

Bravo AF: 0.0896

Asia WGS AF: 0.0460 AC: 160 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	8.5
Dann	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11621151; hg19: chr14-29024101;