10-16553397-A-G

Variant names:

• chr10-16553397-A-G
• rs7084722

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 152,090 control chromosomes in the GnomAD database, including 12,581 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 (12581 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.02

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.562 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: 0.380 AC: 57701 AN: 151972 Hom.: 12587 Cov.: 32

Gnomad AFR AF: 0.164

Gnomad AMI AF: 0.362

Gnomad AMR AF: 0.405

Gnomad ASJ AF: 0.437

Gnomad EAS AF: 0.580

Gnomad SAS AF: 0.497

Gnomad FIN AF: 0.618

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.443

Gnomad OTH AF: 0.371

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

GnomAD4 genome AF: 0.379 AC: 57710 AN: 152090 Hom.: 12581 Cov.: 32 AF XY: 0.390 AC XY: 29002 AN XY: 74338

Gnomad4 AFR AF: 0.164

Gnomad4 AMR AF: 0.405

Gnomad4 ASJ AF: 0.437

Gnomad4 EAS AF: 0.580

Gnomad4 SAS AF: 0.496

Gnomad4 FIN AF: 0.618

Gnomad4 NFE AF: 0.443

Gnomad4 OTH AF: 0.373

Alfa AF: 0.421 Hom.: 18459

Bravo AF: 0.350

Asia WGS AF: 0.510 AC: 1772 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	8.2
DANN	Benign	0.90

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7084722; hg19: chr10-16595396;