11-121788251-T-C

Position:

• chr11-121788251-T-C

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 0.786 in 152,156 control chromosomes in the GnomAD database, including 47,013 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 0.79 (47013 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.958

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.899 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.121788251T>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000286044	ENST00000652518.1	n.140-81071T>C		intron_variant

Frequencies

GnomAD3 genomes AF: 0.786 AC: 119449 AN: 152038 Hom.: 46971 Cov.: 32

Gnomad AFR AF: 0.822

Gnomad AMI AF: 0.748

Gnomad AMR AF: 0.772

Gnomad ASJ AF: 0.776

Gnomad EAS AF: 0.920

Gnomad SAS AF: 0.775

Gnomad FIN AF: 0.765

Gnomad MID AF: 0.763

Gnomad NFE AF: 0.762

Gnomad OTH AF: 0.762

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

GnomAD4 genome AF: 0.786 AC: 119549 AN: 152156 Hom.: 47013 Cov.: 32 AF XY: 0.788 AC XY: 58606 AN XY: 74374

Gnomad4 AFR AF: 0.822

Gnomad4 AMR AF: 0.772

Gnomad4 ASJ AF: 0.776

Gnomad4 EAS AF: 0.921

Gnomad4 SAS AF: 0.774

Gnomad4 FIN AF: 0.765

Gnomad4 NFE AF: 0.762

Gnomad4 OTH AF: 0.765

Alfa AF: 0.761 Hom.: 58299

Bravo AF: 0.789

Asia WGS AF: 0.847 AC: 2946 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.39
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs949076; hg19: chr11-121658959;