10-94890571-A-G

Position:

• chr10-94890571-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 0.776 in 152,072 control chromosomes in the GnomAD database, including 46,073 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 0.78 (46073 hom., cov: 31)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.126

Genes affected

(HGNC:):

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 (SAS) allele frequency at 95% confidence interval = 0.809 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.94890571A>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.776 AC: 117902 AN: 151954 Hom.: 46036 Cov.: 31

Gnomad AFR AF: 0.754

Gnomad AMI AF: 0.867

Gnomad AMR AF: 0.772

Gnomad ASJ AF: 0.751

Gnomad EAS AF: 0.596

Gnomad SAS AF: 0.830

Gnomad FIN AF: 0.866

Gnomad MID AF: 0.633

Gnomad NFE AF: 0.787

Gnomad OTH AF: 0.754

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

GnomAD4 genome AF: 0.776 AC: 117992 AN: 152072 Hom.: 46073 Cov.: 31 AF XY: 0.779 AC XY: 57912 AN XY: 74334

Gnomad4 AFR AF: 0.754

Gnomad4 AMR AF: 0.772

Gnomad4 ASJ AF: 0.751

Gnomad4 EAS AF: 0.595

Gnomad4 SAS AF: 0.831

Gnomad4 FIN AF: 0.866

Gnomad4 NFE AF: 0.787

Gnomad4 OTH AF: 0.756

Alfa AF: 0.785 Hom.: 10324

Bravo AF: 0.764

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	4.5
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4110517; hg19: chr10-96650328;