11-68030238-C-G

Variant names:

• chr11-68030238-C-G
• rs10896288
• ENST00000532296.1:n.203+21G>C

Variant summary

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

The ENST00000532296.1(ENSG00000255306):​n.203+21G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.452 in 151,838 control chromosomes in the GnomAD database, including 18,521 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 0.45 (18458 hom., cov: 30)
  • Exomes 𝑓: 0.64 (63 hom.)
• Consequence: ENSG00000255306 ENST00000532296.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0310

Genes affected

ENSG00000255306 (HGNC:56861):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.661 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
ENSG00000255306	ENST00000532296.1	n.203+21G>C		intron_variant	Intron 1 of 3	3

Frequencies

GnomAD3 genomes AF: 0.452 AC: 68421 AN: 151448 Hom.: 18457 Cov.: 30

Gnomad AFR AF: 0.132

Gnomad AMI AF: 0.535

Gnomad AMR AF: 0.583

Gnomad ASJ AF: 0.594

Gnomad EAS AF: 0.554

Gnomad SAS AF: 0.682

Gnomad FIN AF: 0.573

Gnomad MID AF: 0.646

Gnomad NFE AF: 0.563

Gnomad OTH AF: 0.499

GnomAD4 exome AF: 0.639 AC: 175 AN: 274 Hom.: 63 Cov.: 0 AF XY: 0.656 AC XY: 143 AN XY: 218

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 1.00

Gnomad4 SAS exome AF: 0.677

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.586

Gnomad4 OTH exome AF: 0.333

GnomAD4 genome AF: 0.451 AC: 68416 AN: 151564 Hom.: 18458 Cov.: 30 AF XY: 0.459 AC XY: 33994 AN XY: 74024

Gnomad4 AFR AF: 0.132

Gnomad4 AMR AF: 0.583

Gnomad4 ASJ AF: 0.594

Gnomad4 EAS AF: 0.554

Gnomad4 SAS AF: 0.681

Gnomad4 FIN AF: 0.573

Gnomad4 NFE AF: 0.563

Gnomad4 OTH AF: 0.503

Alfa AF: 0.378 Hom.: 1201

Bravo AF: 0.437

Asia WGS AF: 0.584 AC: 2031 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	3.8
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10896288; hg19: chr11-67797705;