3-110070723-A-G

Variant names:

• chr3-110070723-A-G
• rs10934011

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 0.722 in 152,100 control chromosomes in the GnomAD database, including 40,609 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 0.72 (40609 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.915
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.834 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.722 AC: 109710 AN: 151982 Hom.: 40601 Cov.: 32

Gnomad AFR AF: 0.544

Gnomad AMI AF: 0.814

Gnomad AMR AF: 0.700

Gnomad ASJ AF: 0.780

Gnomad EAS AF: 0.811

Gnomad SAS AF: 0.856

Gnomad FIN AF: 0.813

Gnomad MID AF: 0.810

Gnomad NFE AF: 0.799

Gnomad OTH AF: 0.728

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

GnomAD4 genome AF: 0.722 AC: 109744 AN: 152100 Hom.: 40609 Cov.: 32 AF XY: 0.724 AC XY: 53819 AN XY: 74356

African (AFR) AF: 0.544 AC: 22535 AN: 41452

American (AMR) AF: 0.701 AC: 10718 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.780 AC: 2705 AN: 3470

East Asian (EAS) AF: 0.811 AC: 4182 AN: 5156

South Asian (SAS) AF: 0.856 AC: 4131 AN: 4826

European-Finnish (FIN) AF: 0.813 AC: 8606 AN: 10584

Middle Eastern (MID) AF: 0.813 AC: 239 AN: 294

European-Non Finnish (NFE) AF: 0.799 AC: 54348 AN: 68002

Other (OTH) AF: 0.728 AC: 1538 AN: 2112

Alfa AF: 0.778 Hom.: 197619

Bravo AF: 0.705

Asia WGS AF: 0.804 AC: 2796 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	5.6
DANN	Benign	0.72
PhyloP100		0.92

Splicing

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

Other links and lift over

dbSNP: rs10934011; hg19: chr3-109789570;