11-102930574-T-G

Position:

• chr11-102930574-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 0.327 in 152,114 control chromosomes in the GnomAD database, including 9,940 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 0.33 (9940 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.606

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 (NFE) allele frequency at 95% confidence interval = 0.429 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: 0.327 AC: 49674 AN: 151996 Hom.: 9937 Cov.: 32

Gnomad AFR AF: 0.0949

Gnomad AMI AF: 0.454

Gnomad AMR AF: 0.410

Gnomad ASJ AF: 0.332

Gnomad EAS AF: 0.208

Gnomad SAS AF: 0.412

Gnomad FIN AF: 0.439

Gnomad MID AF: 0.312

Gnomad NFE AF: 0.433

Gnomad OTH AF: 0.338

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

GnomAD4 genome AF: 0.327 AC: 49677 AN: 152114 Hom.: 9940 Cov.: 32 AF XY: 0.328 AC XY: 24403 AN XY: 74350

Gnomad4 AFR AF: 0.0947

Gnomad4 AMR AF: 0.410

Gnomad4 ASJ AF: 0.332

Gnomad4 EAS AF: 0.208

Gnomad4 SAS AF: 0.411

Gnomad4 FIN AF: 0.439

Gnomad4 NFE AF: 0.433

Gnomad4 OTH AF: 0.333

Alfa AF: 0.401 Hom.: 12895

Bravo AF: 0.315

Asia WGS AF: 0.274 AC: 953 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	4.4
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12792912; hg19: chr11-102801303;