rs1147882

Variant names:

• chr10-44350983-C-A
• rs1147882
• XR_007062369.1:n.307G>T

Your query was ambiguous. Multiple possible variants found:

• chr10-44350983-C-A
• chr10-44350983-C-T

Variant summary

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

The XR_007062369.1(LOC124902544):​n.307G>T 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 0.426 in 152,068 control chromosomes in the GnomAD database, including 15,139 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 0.43 (15139 hom., cov: 33)
• Consequence: LOC124902544 XR_007062369.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.44
• Publications: 5 publications found

Genes affected

LOC124902544 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.602 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: 0.426 AC: 64759 AN: 151950 Hom.: 15132 Cov.: 33

Gnomad AFR AF: 0.225

Gnomad AMI AF: 0.690

Gnomad AMR AF: 0.422

Gnomad ASJ AF: 0.500

Gnomad EAS AF: 0.620

Gnomad SAS AF: 0.446

Gnomad FIN AF: 0.462

Gnomad MID AF: 0.455

Gnomad NFE AF: 0.520

Gnomad OTH AF: 0.441

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

GnomAD4 genome AF: 0.426 AC: 64769 AN: 152068 Hom.: 15139 Cov.: 33 AF XY: 0.423 AC XY: 31421 AN XY: 74324

African (AFR) AF: 0.224 AC: 9297 AN: 41476

American (AMR) AF: 0.422 AC: 6453 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.500 AC: 1735 AN: 3470

East Asian (EAS) AF: 0.619 AC: 3194 AN: 5156

South Asian (SAS) AF: 0.445 AC: 2145 AN: 4820

European-Finnish (FIN) AF: 0.462 AC: 4887 AN: 10568

Middle Eastern (MID) AF: 0.442 AC: 129 AN: 292

European-Non Finnish (NFE) AF: 0.520 AC: 35351 AN: 67978

Other (OTH) AF: 0.449 AC: 949 AN: 2114

Alfa AF: 0.473 Hom.: 2204

Bravo AF: 0.414

Asia WGS AF: 0.541 AC: 1877 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.063
DANN	Benign	0.35
PhyloP100		-1.4
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs1147882; hg19: chr10-44846431;