rs12249281

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr10-5033301-G-A
• chr10-5033301-G-C
• chr10-5033301-G-T

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107984198	XR_001747341.2	n.235G>A		non_coding_transcript_exon_variant	Exon 1 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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 v4.3

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;