10-5033301-G-A

Variant names:

• chr10-5033301-G-A
• rs12249281
• XR_001747341.2:n.235G>A

Variant summary

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

The XR_001747341.2(LOC107984198):​n.235G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.509 in 152,000 control chromosomes in the GnomAD database, including 20,074 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 0.51 (20074 hom., cov: 32)
• Consequence: LOC107984198 XR_001747341.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.704
• Publications: 5 publications found

Genes affected

LOC107984198 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.774 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: 0.509 AC: 77343 AN: 151882 Hom.: 20065 Cov.: 32

Gnomad AFR AF: 0.504

Gnomad AMI AF: 0.318

Gnomad AMR AF: 0.439

Gnomad ASJ AF: 0.538

Gnomad EAS AF: 0.795

Gnomad SAS AF: 0.574

Gnomad FIN AF: 0.496

Gnomad MID AF: 0.598

Gnomad NFE AF: 0.504

Gnomad OTH AF: 0.523

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

GnomAD4 genome AF: 0.509 AC: 77401 AN: 152000 Hom.: 20074 Cov.: 32 AF XY: 0.508 AC XY: 37771 AN XY: 74290

African (AFR) AF: 0.504 AC: 20863 AN: 41418

American (AMR) AF: 0.439 AC: 6710 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.538 AC: 1866 AN: 3470

East Asian (EAS) AF: 0.795 AC: 4106 AN: 5168

South Asian (SAS) AF: 0.573 AC: 2762 AN: 4820

European-Finnish (FIN) AF: 0.496 AC: 5239 AN: 10560

Middle Eastern (MID) AF: 0.595 AC: 175 AN: 294

European-Non Finnish (NFE) AF: 0.504 AC: 34277 AN: 67972

Other (OTH) AF: 0.527 AC: 1113 AN: 2110

Alfa AF: 0.509 Hom.: 71480

Bravo AF: 0.504

Asia WGS AF: 0.658 AC: 2287 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	5.3
DANN	Benign	0.46
PhyloP100		-0.70

Splicing

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

Other links and lift over

dbSNP: rs12249281; hg19: chr10-5075493;