rs10937331

Variant names:

• chr3-188030289-A-G
• rs10937331
• XR_001741061.2:n.162+11829T>C

Variant summary

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

The XR_001741061.2(LOC107986166):​n.162+11829T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.342 in 152,028 control chromosomes in the GnomAD database, including 9,577 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 0.34 (9577 hom., cov: 31)
• Consequence: LOC107986166 XR_001741061.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0500
• Publications: 7 publications found

Genes affected

LOC107986166 (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 (NFE) allele frequency at 95% confidence interval = 0.409 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: 0.342 AC: 51992 AN: 151910 Hom.: 9572 Cov.: 31

Gnomad AFR AF: 0.220

Gnomad AMI AF: 0.470

Gnomad AMR AF: 0.348

Gnomad ASJ AF: 0.471

Gnomad EAS AF: 0.190

Gnomad SAS AF: 0.272

Gnomad FIN AF: 0.402

Gnomad MID AF: 0.405

Gnomad NFE AF: 0.413

Gnomad OTH AF: 0.377

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

GnomAD4 genome AF: 0.342 AC: 52014 AN: 152028 Hom.: 9577 Cov.: 31 AF XY: 0.340 AC XY: 25295 AN XY: 74294

African (AFR) AF: 0.220 AC: 9140 AN: 41470

American (AMR) AF: 0.348 AC: 5318 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.471 AC: 1634 AN: 3470

East Asian (EAS) AF: 0.190 AC: 984 AN: 5172

South Asian (SAS) AF: 0.273 AC: 1316 AN: 4826

European-Finnish (FIN) AF: 0.402 AC: 4232 AN: 10540

Middle Eastern (MID) AF: 0.408 AC: 120 AN: 294

European-Non Finnish (NFE) AF: 0.413 AC: 28054 AN: 67950

Other (OTH) AF: 0.374 AC: 788 AN: 2106

Alfa AF: 0.372 Hom.: 1878

Bravo AF: 0.336

Asia WGS AF: 0.214 AC: 750 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	2.2
DANN	Benign	0.40
PhyloP100		0.050

Splicing

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

Other links and lift over

dbSNP: rs10937331; hg19: chr3-187748077;