11-86703240-A-G

Variant names:

• chr11-86703240-A-G
• rs2512987
• ENST00000526206.1:n.29+113A>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 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: ENSG00000254731 ENST00000526206.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.283

Genes affected

ENSG00000254731 (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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000254731	ENST00000526206.1	n.29+113A>G		intron_variant	Intron 1 of 1	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;