rs113413

Variant names:

• chr22-23950077-T-C
• rs113413
• ENST00000440099.1:n.88+72T>C

Your query was ambiguous. Multiple possible variants found:

• chr22-23950077-T-C
• chr22-23950077-T-G

Variant summary

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

The ENST00000703580.1(ENSG00000290199):​n.310-23557A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.561 in 706 control chromosomes in the GnomAD database, including 54 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 0.60 (14837 hom., cov: 39)
  • Exomes 𝑓: 0.56 (54 hom.)
  • Failed GnomAD Quality Control
• Consequence: ENSG00000290199 ENST00000703580.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0420

Genes affected

ENSG00000231271 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAdExome4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.514 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
ENSG00000231271	ENST00000440099.1	n.88+72T>C		intron_variant	Intron 1 of 2	6
ENSG00000290199	ENST00000703580.1	n.310-23557A>G		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.00 AC: 84188 AN: 141026 Hom.: 14798 Cov.: 39 FAILED QC

Gnomad AFR AF: 0.714

Gnomad AMI AF: 0.477

Gnomad AMR AF: 0.551

Gnomad ASJ AF: 0.569

Gnomad EAS AF: 0.638

Gnomad SAS AF: 0.529

Gnomad FIN AF: 0.552

Gnomad MID AF: 0.549

Gnomad NFE AF: 0.550

Gnomad OTH AF: 0.578

GnomAD4 exome AF: 0.561 AC: 396 AN: 706 Hom.: 54 AF XY: 0.574 AC XY: 233 AN XY: 406

Gnomad4 AFR exome AF: 0.500

Gnomad4 EAS exome AF: 0.917

Gnomad4 SAS exome AF: 0.429

Gnomad4 FIN exome AF: 0.570

Gnomad4 NFE exome AF: 0.393

Gnomad4 OTH exome AF: 0.400

GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.597 AC: 84276 AN: 141128 Hom.: 14837 Cov.: 39 AF XY: 0.594 AC XY: 40935 AN XY: 68924

Gnomad4 AFR AF: 0.714

Gnomad4 AMR AF: 0.551

Gnomad4 ASJ AF: 0.569

Gnomad4 EAS AF: 0.639

Gnomad4 SAS AF: 0.528

Gnomad4 FIN AF: 0.552

Gnomad4 NFE AF: 0.550

Gnomad4 OTH AF: 0.580

Alfa AF: 0.402 Hom.: 4043

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	4.1
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs113413; hg19: chr22-24292264;