10-99524480-T-G

Position:

• chr10-99524480-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.502 in 151,868 control chromosomes in the GnomAD database, including 19,411 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 0.50 (19411 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.465

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.55).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.609 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

Frequencies

GnomAD3 genomes AF: 0.502 AC: 76237 AN: 151750 Hom.: 19387 Cov.: 31

Gnomad AFR AF: 0.441

Gnomad AMI AF: 0.481

Gnomad AMR AF: 0.557

Gnomad ASJ AF: 0.461

Gnomad EAS AF: 0.552

Gnomad SAS AF: 0.628

Gnomad FIN AF: 0.511

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.517

Gnomad OTH AF: 0.487

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

GnomAD4 genome AF: 0.502 AC: 76300 AN: 151868 Hom.: 19411 Cov.: 31 AF XY: 0.506 AC XY: 37561 AN XY: 74206

Gnomad4 AFR AF: 0.441

Gnomad4 AMR AF: 0.558

Gnomad4 ASJ AF: 0.461

Gnomad4 EAS AF: 0.552

Gnomad4 SAS AF: 0.627

Gnomad4 FIN AF: 0.511

Gnomad4 NFE AF: 0.517

Gnomad4 OTH AF: 0.483

Alfa AF: 0.506 Hom.: 34675

Bravo AF: 0.501

Asia WGS AF: 0.594 AC: 2064 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.55
CADD	Benign	15
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4409764; hg19: chr10-101284237;