rs1023262

chr10-44398416-A-Gchr10-44398416-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_001747298.2(LOC107984179):n.188+139A>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.681 in 152,190 control chromosomes in the GnomAD database, including 37,906 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 0.68 (37906 hom., cov: 34)
• Consequence: LOC107984179 XR_001747298.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0190

Genes affected

LOC107984179 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.848 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107984179	XR_001747298.2	n.188+139A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.681 AC: 103606 AN: 152072 Hom.: 37896 Cov.: 34

Gnomad AFR AF: 0.387

Gnomad AMI AF: 0.823

Gnomad AMR AF: 0.779

Gnomad ASJ AF: 0.761

Gnomad EAS AF: 0.869

Gnomad SAS AF: 0.764

Gnomad FIN AF: 0.822

Gnomad MID AF: 0.774

Gnomad NFE AF: 0.789

Gnomad OTH AF: 0.722

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

GnomAD4 genome AF: 0.681 AC: 103648 AN: 152190 Hom.: 37906 Cov.: 34 AF XY: 0.687 AC XY: 51130 AN XY: 74418

Gnomad4 AFR AF: 0.386

Gnomad4 AMR AF: 0.779

Gnomad4 ASJ AF: 0.761

Gnomad4 EAS AF: 0.869

Gnomad4 SAS AF: 0.764

Gnomad4 FIN AF: 0.822

Gnomad4 NFE AF: 0.789

Gnomad4 OTH AF: 0.725

Alfa AF: 0.754 Hom.: 31674

Bravo AF: 0.667

Asia WGS AF: 0.808 AC: 2810 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	1.8
Dann	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1023262; hg19: chr10-44893864;