chr11-5230954-T-A

Position:

• chr11-5230954-T-A

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 0.0972 in 152,030 control chromosomes in the GnomAD database, including 2,216 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 0.097 (2216 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.13

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.321 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: 0.0970 AC: 14736 AN: 151914 Hom.: 2206 Cov.: 31

Gnomad AFR AF: 0.326

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0417

Gnomad ASJ AF: 0.00173

Gnomad EAS AF: 0.000386

Gnomad SAS AF: 0.00394

Gnomad FIN AF: 0.00339

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.00616

Gnomad OTH AF: 0.0789

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

GnomAD4 genome AF: 0.0972 AC: 14781 AN: 152030 Hom.: 2216 Cov.: 31 AF XY: 0.0934 AC XY: 6947 AN XY: 74354

Gnomad4 AFR AF: 0.326

Gnomad4 AMR AF: 0.0416

Gnomad4 ASJ AF: 0.00173

Gnomad4 EAS AF: 0.000387

Gnomad4 SAS AF: 0.00373

Gnomad4 FIN AF: 0.00339

Gnomad4 NFE AF: 0.00616

Gnomad4 OTH AF: 0.0781

Alfa AF: 0.00393 Hom.: 7

Bravo AF: 0.107

Asia WGS AF: 0.0220 AC: 78 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.5
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7112844; hg19: chr11-5252184;