10-73949409-TTTTATTTATTTATTTA-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 0.011 (29 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 afr. gnomad4 allele frequency = 0.0111 (1501/134946) while in subpopulation AFR AF= 0.0368 (1330/36122). AF 95% confidence interval is 0.0352. There are 29 homozygotes in gnomad4. There are 737 alleles in male gnomad4 subpopulation. Median coverage is 0. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd at 29 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: 0.0111 AC: 1493 AN: 134908 Hom.: 29 Cov.: 0

Gnomad AFR AF: 0.0367

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00482

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00196

Gnomad SAS AF: 0.00220

Gnomad FIN AF: 0.000705

Gnomad MID AF: 0.00333

Gnomad NFE AF: 0.00105

Gnomad OTH AF: 0.00970

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

GnomAD4 genome AF: 0.0111 AC: 1501 AN: 134946 Hom.: 29 Cov.: 0 AF XY: 0.0114 AC XY: 737 AN XY: 64620

Gnomad4 AFR AF: 0.0368

Gnomad4 AMR AF: 0.00482

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00197

Gnomad4 SAS AF: 0.00221

Gnomad4 FIN AF: 0.000705

Gnomad4 NFE AF: 0.00105

Gnomad4 OTH AF: 0.00960

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;