rs7100467

Variant names:

• chr10-106403450-G-A
• rs7100467

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;