chr11-5231021-T-C

Position:

• chr11-5231021-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 0.577 in 151,816 control chromosomes in the GnomAD database, including 26,109 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 0.58 (26109 hom., cov: 30)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.928

Genes affected

(HGNC:):

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 (EAS) allele frequency at 95% confidence interval = 0.759 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.5231021T>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.577 AC: 87543 AN: 151698 Hom.: 26061 Cov.: 30

Gnomad AFR AF: 0.692

Gnomad AMI AF: 0.490

Gnomad AMR AF: 0.654

Gnomad ASJ AF: 0.657

Gnomad EAS AF: 0.779

Gnomad SAS AF: 0.552

Gnomad FIN AF: 0.445

Gnomad MID AF: 0.658

Gnomad NFE AF: 0.493

Gnomad OTH AF: 0.613

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

GnomAD4 genome AF: 0.577 AC: 87654 AN: 151816 Hom.: 26109 Cov.: 30 AF XY: 0.578 AC XY: 42847 AN XY: 74170

Gnomad4 AFR AF: 0.692

Gnomad4 AMR AF: 0.654

Gnomad4 ASJ AF: 0.657

Gnomad4 EAS AF: 0.780

Gnomad4 SAS AF: 0.553

Gnomad4 FIN AF: 0.445

Gnomad4 NFE AF: 0.493

Gnomad4 OTH AF: 0.615

Alfa AF: 0.523 Hom.: 3878

Bravo AF: 0.595

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.1
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: rs6578588; hg19: chr11-5252251; COSMIC: COSV53082830;