rs7100467

Positions:

• chr10-106403450-G-A

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 0.0812 in 152,074 control chromosomes in the GnomAD database, including 863 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 0.081 (863 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.72

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.183 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: 0.0813 AC: 12348 AN: 151956 Hom.: 861 Cov.: 32

Gnomad AFR AF: 0.187

Gnomad AMI AF: 0.0329

Gnomad AMR AF: 0.0474

Gnomad ASJ AF: 0.0788

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.0647

Gnomad FIN AF: 0.00868

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.0442

Gnomad OTH AF: 0.0756

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

GnomAD4 genome AF: 0.0812 AC: 12356 AN: 152074 Hom.: 863 Cov.: 32 AF XY: 0.0781 AC XY: 5811 AN XY: 74370

Gnomad4 AFR AF: 0.187

Gnomad4 AMR AF: 0.0472

Gnomad4 ASJ AF: 0.0788

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.0654

Gnomad4 FIN AF: 0.00868

Gnomad4 NFE AF: 0.0442

Gnomad4 OTH AF: 0.0748

Alfa AF: 0.0632 Hom.: 82

Bravo AF: 0.0871

Asia WGS AF: 0.0350 AC: 124 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.045
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7100467; hg19: chr10-108163208;