10-45374099-TGCGGGGGCGGGGGCGGGGGCGGGG-TGCGGGGGCGGGGGCGGGGGCGGGGGCGGGGGCGGGG

Position:

• chr10-45374099-TGCGGGGGCGGGGGCGGGGGCGGGG-TGCGGGGGCGGGGGCGGGGGCGGGGGCGGGGGCGGGG

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2

The variant allele was found at a frequency of 0.00153 in 821,954 control chromosomes in the GnomAD database, including 11 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.0051 (10 hom., cov: 22)
  • Exomes 𝑓: 0.00072 (1 hom.)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.292

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BS2: High Homozygotes in GnomAd4 at 10 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.00513 AC: 769 AN: 149884 Hom.: 10 Cov.: 22

Gnomad AFR AF: 0.0102

Gnomad AMI AF: 0.0748

Gnomad AMR AF: 0.00521

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00950

Gnomad SAS AF: 0.00212

Gnomad FIN AF: 0.0000969

Gnomad MID AF: 0.00323

Gnomad NFE AF: 0.00208

Gnomad OTH AF: 0.00533

GnomAD4 exome AF: 0.000723 AC: 486 AN: 671966 Hom.: 1 AF XY: 0.000700 AC XY: 228 AN XY: 325604

Gnomad4 AFR exome AF: 0.00397

Gnomad4 AMR exome AF: 0.00225

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00416

Gnomad4 SAS exome AF: 0.000629

Gnomad4 FIN exome AF: 0.000193

Gnomad4 NFE exome AF: 0.000470

Gnomad4 OTH exome AF: 0.00171

GnomAD4 genome AF: 0.00515 AC: 772 AN: 149988 Hom.: 10 Cov.: 22 AF XY: 0.00484 AC XY: 354 AN XY: 73136

Gnomad4 AFR AF: 0.0102

Gnomad4 AMR AF: 0.00521

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00953

Gnomad4 SAS AF: 0.00213

Gnomad4 FIN AF: 0.0000969

Gnomad4 NFE AF: 0.00208

Gnomad4 OTH AF: 0.00528

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs59439148; hg19: chr10-45869547;