rs3123078

Variant names:

• chr10-46070851-G-A
• rs3123078

Your query was ambiguous. Multiple possible variants found:

• chr10-46070851-G-A
• chr10-46070851-G-C

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 0.549 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.549 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

Gnomad4 AFR AF: 0.530

Gnomad4 AMR AF: 0.587

Gnomad4 ASJ AF: 0.454

Gnomad4 EAS AF: 0.541

Gnomad4 SAS AF: 0.422

Gnomad4 FIN AF: 0.615

Gnomad4 NFE AF: 0.559

Gnomad4 OTH AF: 0.532

Alfa AF: 0.545 Hom.: 46472

Bravo AF: 0.552

Asia WGS AF: 0.483 AC: 1681 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3123078; hg19: chr10-51524971;