11-86703240-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000526206.1(ENSG00000254731):n.29+113A>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.467 in 152,022 control chromosomes in the GnomAD database, including 16,795 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 0.47 (16785 hom., cov: 32)
  • Exomes 𝑓: 0.55 (10 hom.)
• Consequence: ENST00000526206.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.283

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.479 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
	ENST00000526206.1	n.29+113A>G		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.467 AC: 70864 AN: 151842 Hom.: 16776 Cov.: 32

Gnomad AFR AF: 0.485

Gnomad AMI AF: 0.342

Gnomad AMR AF: 0.391

Gnomad ASJ AF: 0.400

Gnomad EAS AF: 0.307

Gnomad SAS AF: 0.451

Gnomad FIN AF: 0.581

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.476

Gnomad OTH AF: 0.429

GnomAD4 exome AF: 0.545 AC: 36 AN: 66 Hom.: 10 AF XY: 0.533 AC XY: 16 AN XY: 30

Gnomad4 ASJ exome AF: 0.500

Gnomad4 FIN exome AF: 0.536

Gnomad4 NFE exome AF: 0.625

GnomAD4 genome AF: 0.467 AC: 70915 AN: 151956 Hom.: 16785 Cov.: 32 AF XY: 0.467 AC XY: 34704 AN XY: 74280

Gnomad4 AFR AF: 0.484

Gnomad4 AMR AF: 0.391

Gnomad4 ASJ AF: 0.400

Gnomad4 EAS AF: 0.307

Gnomad4 SAS AF: 0.452

Gnomad4 FIN AF: 0.581

Gnomad4 NFE AF: 0.475

Gnomad4 OTH AF: 0.427

Alfa AF: 0.459 Hom.: 27095

Bravo AF: 0.450

Asia WGS AF: 0.397 AC: 1379 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	1.2
Dann	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2512987; hg19: chr11-86414282;