rs1147882

Positions:

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

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

LOC124902544 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
LOC124902544	XR_007062369.1	n.307G>T		non_coding_transcript_exon_variant	1/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.224

Gnomad4 AMR AF: 0.422

Gnomad4 ASJ AF: 0.500

Gnomad4 EAS AF: 0.619

Gnomad4 SAS AF: 0.445

Gnomad4 FIN AF: 0.462

Gnomad4 NFE AF: 0.520

Gnomad4 OTH AF: 0.449

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1147882; hg19: chr10-44846431;