10-84044676-A-G

Position:

• chr10-84044676-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 0.307 in 152,176 control chromosomes in the GnomAD database, including 8,044 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 0.31 (8044 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.00

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.453 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: 0.306 AC: 46587 AN: 152058 Hom.: 8022 Cov.: 32

Gnomad AFR AF: 0.459

Gnomad AMI AF: 0.269

Gnomad AMR AF: 0.309

Gnomad ASJ AF: 0.406

Gnomad EAS AF: 0.114

Gnomad SAS AF: 0.237

Gnomad FIN AF: 0.209

Gnomad MID AF: 0.396

Gnomad NFE AF: 0.243

Gnomad OTH AF: 0.297

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

GnomAD4 genome AF: 0.307 AC: 46665 AN: 152176 Hom.: 8044 Cov.: 32 AF XY: 0.303 AC XY: 22546 AN XY: 74402

Gnomad4 AFR AF: 0.459

Gnomad4 AMR AF: 0.310

Gnomad4 ASJ AF: 0.406

Gnomad4 EAS AF: 0.114

Gnomad4 SAS AF: 0.237

Gnomad4 FIN AF: 0.209

Gnomad4 NFE AF: 0.243

Gnomad4 OTH AF: 0.295

Alfa AF: 0.273 Hom.: 1851

Bravo AF: 0.318

Asia WGS AF: 0.202 AC: 705 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.091
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7923749; hg19: chr10-85804432;