11-102930574-T-G

Variant names:

• chr11-102930574-T-G
• rs12792912

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 10 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.0947 AC: 3932 AN: 41524

American (AMR) AF: 0.410 AC: 6261 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.332 AC: 1151 AN: 3470

East Asian (EAS) AF: 0.208 AC: 1078 AN: 5180

South Asian (SAS) AF: 0.411 AC: 1980 AN: 4812

European-Finnish (FIN) AF: 0.439 AC: 4635 AN: 10558

Middle Eastern (MID) AF: 0.322 AC: 94 AN: 292

European-Non Finnish (NFE) AF: 0.433 AC: 29428 AN: 67980

Other (OTH) AF: 0.333 AC: 705 AN: 2116

Alfa AF: 0.397 Hom.: 18667

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
PhyloP100		0.61

Splicing

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

Other links and lift over

dbSNP: rs12792912; hg19: chr11-102801303;