3-70581456-A-T

Variant names:

• chr3-70581456-A-T
• rs9310194
• XR_001740559.2:n.210-2782T>A

Variant summary

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

The XR_001740559.2(LOC105377152):​n.210-2782T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.245 in 151,778 control chromosomes in the GnomAD database, including 4,879 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 0.25 (4879 hom., cov: 31)
• Consequence: LOC105377152 XR_001740559.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.491
• Publications: 2 publications found

Genes affected

LOC105377152 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.535 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.245 AC: 37183 AN: 151660 Hom.: 4869 Cov.: 31

Gnomad AFR AF: 0.224

Gnomad AMI AF: 0.182

Gnomad AMR AF: 0.235

Gnomad ASJ AF: 0.210

Gnomad EAS AF: 0.551

Gnomad SAS AF: 0.383

Gnomad FIN AF: 0.285

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.224

Gnomad OTH AF: 0.238

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

GnomAD4 genome AF: 0.245 AC: 37231 AN: 151778 Hom.: 4879 Cov.: 31 AF XY: 0.250 AC XY: 18514 AN XY: 74124

African (AFR) AF: 0.225 AC: 9314 AN: 41436

American (AMR) AF: 0.236 AC: 3585 AN: 15202

Ashkenazi Jewish (ASJ) AF: 0.210 AC: 727 AN: 3470

East Asian (EAS) AF: 0.551 AC: 2830 AN: 5132

South Asian (SAS) AF: 0.382 AC: 1838 AN: 4810

European-Finnish (FIN) AF: 0.285 AC: 3010 AN: 10554

Middle Eastern (MID) AF: 0.160 AC: 47 AN: 294

European-Non Finnish (NFE) AF: 0.224 AC: 15201 AN: 67862

Other (OTH) AF: 0.244 AC: 513 AN: 2106

Alfa AF: 0.227 Hom.: 517

Bravo AF: 0.244

Asia WGS AF: 0.447 AC: 1553 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.92
DANN	Benign	0.62
PhyloP100		-0.49

Splicing

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

Other links and lift over

dbSNP: rs9310194; hg19: chr3-70630607;