10-99777984-T-G

Variant names:

• chr10-99777984-T-G
• rs2180989

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 0.376 in 152,016 control chromosomes in the GnomAD database, including 11,223 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 (11223 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.181

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.72).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.423 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.376 AC: 57171 AN: 151898 Hom.: 11219 Cov.: 32

Gnomad AFR AF: 0.288

Gnomad AMI AF: 0.524

Gnomad AMR AF: 0.412

Gnomad ASJ AF: 0.470

Gnomad EAS AF: 0.230

Gnomad SAS AF: 0.374

Gnomad FIN AF: 0.363

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.427

Gnomad OTH AF: 0.417

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

GnomAD4 genome AF: 0.376 AC: 57190 AN: 152016 Hom.: 11223 Cov.: 32 AF XY: 0.374 AC XY: 27762 AN XY: 74284

Gnomad4 AFR AF: 0.288

Gnomad4 AMR AF: 0.412

Gnomad4 ASJ AF: 0.470

Gnomad4 EAS AF: 0.229

Gnomad4 SAS AF: 0.374

Gnomad4 FIN AF: 0.363

Gnomad4 NFE AF: 0.427

Gnomad4 OTH AF: 0.420

Alfa AF: 0.393 Hom.: 1480

Bravo AF: 0.374

Asia WGS AF: 0.330 AC: 1147 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	7.2
DANN	Benign	0.93

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2180989; hg19: chr10-101537741;