10-94890571-A-G

Variant names:

• chr10-94890571-A-G
• rs4110517

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: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.126

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;