rs113413

Positions:

• 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 ENST00000440099.1(ENSG00000231271):​n.88+72T>C 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 0.561 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: ENST00000440099.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0420

Genes affected

(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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000440099.1	n.88+72T>C		intron_variant, non_coding_transcript_variant

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;