11-102881122-T-G

Position:

• chr11-102881122-T-G

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 0.051 in 144,668 control chromosomes in the GnomAD database, including 780 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 0.051 (780 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.38

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0596 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: 0.0510 AC: 7377 AN: 144566 Hom.: 778 Cov.: 29

Gnomad AFR AF: 0.0470

Gnomad AMI AF: 0.0504

Gnomad AMR AF: 0.0334

Gnomad ASJ AF: 0.0608

Gnomad EAS AF: 0.0274

Gnomad SAS AF: 0.0655

Gnomad FIN AF: 0.0535

Gnomad MID AF: 0.105

Gnomad NFE AF: 0.0570

Gnomad OTH AF: 0.0408

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

GnomAD4 genome AF: 0.0510 AC: 7384 AN: 144668 Hom.: 780 Cov.: 29 AF XY: 0.0498 AC XY: 3525 AN XY: 70734

Gnomad4 AFR AF: 0.0471

Gnomad4 AMR AF: 0.0334

Gnomad4 ASJ AF: 0.0608

Gnomad4 EAS AF: 0.0275

Gnomad4 SAS AF: 0.0657

Gnomad4 FIN AF: 0.0535

Gnomad4 NFE AF: 0.0570

Gnomad4 OTH AF: 0.0399

Alfa AF: 0.0619 Hom.: 160

Asia WGS AF: 0.0510 AC: 174 AN: 3384

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.33
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: rs17099726; hg19: chr11-102751852;