chr10-99514708-A-G

Position:

• chr10-99514708-A-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 0.379 in 151,904 control chromosomes in the GnomAD database, including 11,310 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 0.38 (11310 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.197

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.517 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: 0.379 AC: 57466 AN: 151786 Hom.: 11288 Cov.: 32

Gnomad AFR AF: 0.301

Gnomad AMI AF: 0.289

Gnomad AMR AF: 0.452

Gnomad ASJ AF: 0.302

Gnomad EAS AF: 0.534

Gnomad SAS AF: 0.380

Gnomad FIN AF: 0.457

Gnomad MID AF: 0.304

Gnomad NFE AF: 0.391

Gnomad OTH AF: 0.363

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

GnomAD4 genome AF: 0.379 AC: 57532 AN: 151904 Hom.: 11310 Cov.: 32 AF XY: 0.386 AC XY: 28662 AN XY: 74240

Gnomad4 AFR AF: 0.302

Gnomad4 AMR AF: 0.453

Gnomad4 ASJ AF: 0.302

Gnomad4 EAS AF: 0.534

Gnomad4 SAS AF: 0.380

Gnomad4 FIN AF: 0.457

Gnomad4 NFE AF: 0.391

Gnomad4 OTH AF: 0.362

Alfa AF: 0.390 Hom.: 3070

Bravo AF: 0.377

Asia WGS AF: 0.435 AC: 1511 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	9.7
DANN	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7081330; hg19: chr10-101274465;