11-5225245-C-T

Position:

• chr11-5225245-C-T

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BS1 BS2

The ENST00000644706.1(ENSG00000285498):​n.217G>A 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 0.01 in 348,168 control chromosomes in the GnomAD database, including 42 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.0070 (7 hom., cov: 32)
  • Exomes 𝑓: 0.012 (35 hom.)
• Consequence: ENSG00000285498 ENST00000644706.1 non_coding_transcript_exon
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -1.42

Genes affected

ENSG00000285498 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BP6: Variant 11-5225245-C-T is Benign according to our data. Variant chr11-5225245-C-T is described in ClinVar as [Benign]. Clinvar id is 256343.Status of the report is criteria_provided_single_submitter, 1 stars.
• BS1: Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.00697 (1061/152268) while in subpopulation SAS AF= 0.0382 (184/4814). AF 95% confidence interval is 0.0337. There are 7 homozygotes in gnomad4. There are 521 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 7 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.5225245C>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000285498	ENST00000644706.1	n.217G>A		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.00695 AC: 1058 AN: 152150 Hom.: 7 Cov.: 32

Gnomad AFR AF: 0.00164

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00550

Gnomad ASJ AF: 0.0251

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.0376

Gnomad FIN AF: 0.00132

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.00881

Gnomad OTH AF: 0.00910

GnomAD4 exome AF: 0.0124 AC: 2423 AN: 195900 Hom.: 35 Cov.: 0 AF XY: 0.0147 AC XY: 1566 AN XY: 106424

Gnomad4 AFR exome AF: 0.00109

Gnomad4 AMR exome AF: 0.00532

Gnomad4 ASJ exome AF: 0.0273

Gnomad4 EAS exome AF: 0.000366

Gnomad4 SAS exome AF: 0.0313

Gnomad4 FIN exome AF: 0.00294

Gnomad4 NFE exome AF: 0.00861

Gnomad4 OTH exome AF: 0.0105

GnomAD4 genome AF: 0.00697 AC: 1061 AN: 152268 Hom.: 7 Cov.: 32 AF XY: 0.00700 AC XY: 521 AN XY: 74450

Gnomad4 AFR AF: 0.00164

Gnomad4 AMR AF: 0.00549

Gnomad4 ASJ AF: 0.0251

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.0382

Gnomad4 FIN AF: 0.00132

Gnomad4 NFE AF: 0.00881

Gnomad4 OTH AF: 0.00900

Alfa AF: 0.00310 Hom.: 1

Bravo AF: 0.00612

Asia WGS AF: 0.0110 AC: 38 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not specified Benign:1

Benign, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	0.91
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: rs112988270; hg19: chr11-5246475;