11-117103213-G-C

Variant names:

• chr11-117103213-G-C
• rs12269901
• ENST00000442124.1:n.165-11G>C

Variant summary

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

The ENST00000442124.1(ENSG00000224077):​n.165-11G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.413 in 151,816 control chromosomes in the GnomAD database, including 15,108 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 0.41 (15107 hom., cov: 31)
  • Exomes 𝑓: 0.35 (1 hom.)
• Consequence: ENSG00000224077 ENST00000442124.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0320

Genes affected

ENSG00000224077 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.673 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
ENSG00000224077	ENST00000442124.1	n.165-11G>C		intron_variant	Intron 1 of 2	5

Frequencies

GnomAD3 genomes AF: 0.413 AC: 62583 AN: 151672 Hom.: 15070 Cov.: 31

Gnomad AFR AF: 0.679

Gnomad AMI AF: 0.201

Gnomad AMR AF: 0.337

Gnomad ASJ AF: 0.310

Gnomad EAS AF: 0.282

Gnomad SAS AF: 0.422

Gnomad FIN AF: 0.370

Gnomad MID AF: 0.342

Gnomad NFE AF: 0.294

Gnomad OTH AF: 0.359

GnomAD4 exome AF: 0.346 AC: 9 AN: 26 Hom.: 1 Cov.: 0 AF XY: 0.300 AC XY: 6 AN XY: 20

Gnomad4 AMR exome AF: 0.500

Gnomad4 FIN exome AF: 0.500

Gnomad4 NFE exome AF: 0.333

Gnomad4 OTH exome AF: 0.250

GnomAD4 genome AF: 0.413 AC: 62667 AN: 151790 Hom.: 15107 Cov.: 31 AF XY: 0.414 AC XY: 30673 AN XY: 74152

Gnomad4 AFR AF: 0.679

Gnomad4 AMR AF: 0.337

Gnomad4 ASJ AF: 0.310

Gnomad4 EAS AF: 0.282

Gnomad4 SAS AF: 0.421

Gnomad4 FIN AF: 0.370

Gnomad4 NFE AF: 0.294

Gnomad4 OTH AF: 0.358

Alfa AF: 0.193 Hom.: 398

Bravo AF: 0.423

Asia WGS AF: 0.395 AC: 1378 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.9
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12269901; hg19: chr11-116973929;