11-123209897-G-T

Position:

• chr11-123209897-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 0.118 in 152,180 control chromosomes in the GnomAD database, including 2,149 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 0.12 (2149 hom., cov: 31)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.28

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 (AFR) allele frequency at 95% confidence interval = 0.303 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.123209897G>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000254710	ENST00000531681.2	n.306-2480G>T		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.118 AC: 17880 AN: 152062 Hom.: 2146 Cov.: 31

Gnomad AFR AF: 0.308

Gnomad AMI AF: 0.0877

Gnomad AMR AF: 0.0776

Gnomad ASJ AF: 0.0579

Gnomad EAS AF: 0.0179

Gnomad SAS AF: 0.0242

Gnomad FIN AF: 0.0613

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.0384

Gnomad OTH AF: 0.0989

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

GnomAD4 genome AF: 0.118 AC: 17916 AN: 152180 Hom.: 2149 Cov.: 31 AF XY: 0.116 AC XY: 8607 AN XY: 74416

Gnomad4 AFR AF: 0.308

Gnomad4 AMR AF: 0.0774

Gnomad4 ASJ AF: 0.0579

Gnomad4 EAS AF: 0.0180

Gnomad4 SAS AF: 0.0249

Gnomad4 FIN AF: 0.0613

Gnomad4 NFE AF: 0.0384

Gnomad4 OTH AF: 0.0979

Alfa AF: 0.0837 Hom.: 161

Bravo AF: 0.129

Asia WGS AF: 0.0300 AC: 106 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	0.085
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3763894; hg19: chr11-123080605;