chr11-5225282-T-G

Position:

• chr11-5225282-T-G

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The ENST00000644706.1(ENSG00000285498):​n.180A>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.786 in 390,910 control chromosomes in the GnomAD database, including 122,734 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.81 (50180 hom., cov: 32)
  • Exomes 𝑓: 0.77 (72554 hom.)
• Consequence: ENST00000644706.1 non_coding_transcript_exon
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -0.137

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BP6: Variant 11-5225282-T-G is Benign according to our data. Variant chr11-5225282-T-G is described in ClinVar as [Benign]. Clinvar id is 256342.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.858 is higher than 0.05.

Transcripts

RefSeq

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

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000644706.1	n.180A>C		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.808 AC: 122778 AN: 152016 Hom.: 50140 Cov.: 32

Gnomad AFR AF: 0.865

Gnomad AMI AF: 0.969

Gnomad AMR AF: 0.722

Gnomad ASJ AF: 0.848

Gnomad EAS AF: 0.495

Gnomad SAS AF: 0.622

Gnomad FIN AF: 0.778

Gnomad MID AF: 0.864

Gnomad NFE AF: 0.829

Gnomad OTH AF: 0.818

GnomAD4 exome AF: 0.772 AC: 184417 AN: 238776 Hom.: 72554 Cov.: 2 AF XY: 0.760 AC XY: 98364 AN XY: 129344

Gnomad4 AFR exome AF: 0.867

Gnomad4 AMR exome AF: 0.690

Gnomad4 ASJ exome AF: 0.843

Gnomad4 EAS exome AF: 0.498

Gnomad4 SAS exome AF: 0.636

Gnomad4 FIN exome AF: 0.784

Gnomad4 NFE exome AF: 0.829

Gnomad4 OTH exome AF: 0.797

GnomAD4 genome AF: 0.808 AC: 122874 AN: 152134 Hom.: 50180 Cov.: 32 AF XY: 0.799 AC XY: 59451 AN XY: 74366

Gnomad4 AFR AF: 0.865

Gnomad4 AMR AF: 0.722

Gnomad4 ASJ AF: 0.848

Gnomad4 EAS AF: 0.494

Gnomad4 SAS AF: 0.623

Gnomad4 FIN AF: 0.778

Gnomad4 NFE AF: 0.829

Gnomad4 OTH AF: 0.814

Alfa AF: 0.820 Hom.: 49220

Bravo AF: 0.812

Asia WGS AF: 0.570 AC: 1986 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not specified Benign:1

Benign, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

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- -

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Nov 12, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.1
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7110263; hg19: chr11-5246512;