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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124902544	XR_007062369.1	n.307G>T		non_coding_transcript_exon_variant	Exon 1 of 3

Ensembl

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

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 v4.3

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;