10-73949409-T-TTTTA

Position:

• chr10-73949409-T-TTTTA

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 (12 hom., cov: 0)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.143

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0123 (1663/134932) while in subpopulation NFE AF= 0.0175 (1119/63796). AF 95% confidence interval is 0.0167. There are 12 homozygotes in gnomad4. There are 729 alleles in male gnomad4 subpopulation. Median coverage is 0. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 12 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: 0.0123 AC: 1665 AN: 134894 Hom.: 12 Cov.: 0

Gnomad AFR AF: 0.00430

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00949

Gnomad ASJ AF: 0.0178

Gnomad EAS AF: 0.00632

Gnomad SAS AF: 0.0113

Gnomad FIN AF: 0.0151

Gnomad MID AF: 0.0100

Gnomad NFE AF: 0.0176

Gnomad OTH AF: 0.0126

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

GnomAD4 genome AF: 0.0123 AC: 1663 AN: 134932 Hom.: 12 Cov.: 0 AF XY: 0.0113 AC XY: 729 AN XY: 64612

Gnomad4 AFR AF: 0.00429

Gnomad4 AMR AF: 0.00948

Gnomad4 ASJ AF: 0.0178

Gnomad4 EAS AF: 0.00633

Gnomad4 SAS AF: 0.0111

Gnomad4 FIN AF: 0.0151

Gnomad4 NFE AF: 0.0175

Gnomad4 OTH AF: 0.0124

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;