10-73949409-TTTTATTTATTTATTTATTTATTTA-T

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BS1 BS2

No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.012 (13 hom., cov: 0)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.639

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0124 (1680/134966) while in subpopulation NFE AF= 0.0201 (1283/63820). AF 95% confidence interval is 0.0192. There are 13 homozygotes in gnomad4. There are 778 alleles in male gnomad4 subpopulation. Median coverage is 0. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd at 13 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: 0.0124 AC: 1679 AN: 134928 Hom.: 13 Cov.: 0

Gnomad AFR AF: 0.00338

Gnomad AMI AF: 0.0144

Gnomad AMR AF: 0.00567

Gnomad ASJ AF: 0.00905

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.0105

Gnomad FIN AF: 0.0103

Gnomad MID AF: 0.0300

Gnomad NFE AF: 0.0201

Gnomad OTH AF: 0.0188

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0124 AC: 1680 AN: 134966 Hom.: 13 Cov.: 0 AF XY: 0.0120 AC XY: 778 AN XY: 64630

Gnomad4 AFR AF: 0.00338

Gnomad4 AMR AF: 0.00566

Gnomad4 ASJ AF: 0.00905

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.0108

Gnomad4 FIN AF: 0.0103

Gnomad4 NFE AF: 0.0201

Gnomad4 OTH AF: 0.0186

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: rs3998225; hg19: chr10-75709167;