chr3-67310-A-G

Variant names:

• chr3-67310-A-G
• rs9841287
• XR_940533.2:n.124-15A>G

Variant summary

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

The XR_940533.2(LOC105376921):​n.124-15A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.221 in 151,928 control chromosomes in the GnomAD database, including 4,118 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 0.22 (4118 hom., cov: 31)
• Consequence: LOC105376921 XR_940533.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.503
• Publications: 13 publications found

Genes affected

LOC105376921 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.437 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: 0.221 AC: 33501 AN: 151810 Hom.: 4115 Cov.: 31

Gnomad AFR AF: 0.266

Gnomad AMI AF: 0.0800

Gnomad AMR AF: 0.258

Gnomad ASJ AF: 0.197

Gnomad EAS AF: 0.453

Gnomad SAS AF: 0.272

Gnomad FIN AF: 0.221

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.167

Gnomad OTH AF: 0.220

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

GnomAD4 genome AF: 0.221 AC: 33526 AN: 151928 Hom.: 4118 Cov.: 31 AF XY: 0.225 AC XY: 16694 AN XY: 74224

African (AFR) AF: 0.266 AC: 11024 AN: 41438

American (AMR) AF: 0.258 AC: 3939 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.197 AC: 684 AN: 3470

East Asian (EAS) AF: 0.452 AC: 2329 AN: 5148

South Asian (SAS) AF: 0.272 AC: 1302 AN: 4790

European-Finnish (FIN) AF: 0.221 AC: 2335 AN: 10552

Middle Eastern (MID) AF: 0.177 AC: 52 AN: 294

European-Non Finnish (NFE) AF: 0.167 AC: 11325 AN: 67968

Other (OTH) AF: 0.219 AC: 463 AN: 2110

Alfa AF: 0.188 Hom.: 10435

Bravo AF: 0.228

Asia WGS AF: 0.372 AC: 1291 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.43
DANN	Benign	0.66
PhyloP100		-0.50

Splicing

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

Other links and lift over

dbSNP: rs9841287; hg19: chr3-108993;