chr10-46070851-G-A

Variant names:

• chr10-46070851-G-A
• rs3123078

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.549 in 152,000 control chromosomes in the GnomAD database, including 23,095 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 0.55 (23095 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.663
• Publications: 54 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.577 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.549 AC: 83434 AN: 151882 Hom.: 23086 Cov.: 31

Gnomad AFR AF: 0.530

Gnomad AMI AF: 0.492

Gnomad AMR AF: 0.587

Gnomad ASJ AF: 0.454

Gnomad EAS AF: 0.542

Gnomad SAS AF: 0.424

Gnomad FIN AF: 0.615

Gnomad MID AF: 0.405

Gnomad NFE AF: 0.559

Gnomad OTH AF: 0.535

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

GnomAD4 genome AF: 0.549 AC: 83477 AN: 152000 Hom.: 23095 Cov.: 31 AF XY: 0.548 AC XY: 40691 AN XY: 74260

African (AFR) AF: 0.530 AC: 21968 AN: 41448

American (AMR) AF: 0.587 AC: 8963 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.454 AC: 1577 AN: 3470

East Asian (EAS) AF: 0.541 AC: 2792 AN: 5164

South Asian (SAS) AF: 0.422 AC: 2035 AN: 4818

European-Finnish (FIN) AF: 0.615 AC: 6478 AN: 10536

Middle Eastern (MID) AF: 0.418 AC: 123 AN: 294

European-Non Finnish (NFE) AF: 0.559 AC: 37972 AN: 67974

Other (OTH) AF: 0.532 AC: 1122 AN: 2110

Alfa AF: 0.551 Hom.: 104837

Bravo AF: 0.552

Asia WGS AF: 0.483 AC: 1681 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.7
DANN	Benign	0.56
PhyloP100		-0.66

Splicing

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

Other links and lift over

dbSNP: rs3123078; hg19: chr10-51524971;