rs668053

Positions:

• chr11-121437816-G-A
• chr11-121437816-G-C
• chr11-121437816-G-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 0.413 in 152,056 control chromosomes in the GnomAD database, including 14,647 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 0.41 (14647 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.690

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.632 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: 0.413 AC: 62714 AN: 151938 Hom.: 14644 Cov.: 32

Gnomad AFR AF: 0.191

Gnomad AMI AF: 0.508

Gnomad AMR AF: 0.522

Gnomad ASJ AF: 0.516

Gnomad EAS AF: 0.650

Gnomad SAS AF: 0.604

Gnomad FIN AF: 0.508

Gnomad MID AF: 0.475

Gnomad NFE AF: 0.470

Gnomad OTH AF: 0.409

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

GnomAD4 genome AF: 0.413 AC: 62724 AN: 152056 Hom.: 14647 Cov.: 32 AF XY: 0.421 AC XY: 31296 AN XY: 74328

Gnomad4 AFR AF: 0.190

Gnomad4 AMR AF: 0.522

Gnomad4 ASJ AF: 0.516

Gnomad4 EAS AF: 0.650

Gnomad4 SAS AF: 0.605

Gnomad4 FIN AF: 0.508

Gnomad4 NFE AF: 0.470

Gnomad4 OTH AF: 0.415

Alfa AF: 0.463 Hom.: 34901

Bravo AF: 0.398

Asia WGS AF: 0.625 AC: 2172 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.43
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs668053; hg19: chr11-121308525;