rs728142

chr10-44394011-G-A

Variant summary

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

The XR_001747298.2(LOC107984179):n.68-4146G>A 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 0.0689 in 152,244 control chromosomes in the GnomAD database, including 391 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 0.069 (391 hom., cov: 33)
• Consequence: LOC107984179 XR_001747298.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.423

Genes affected

LOC107984179 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0876 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107984179	XR_001747298.2	n.68-4146G>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0690 AC: 10497 AN: 152126 Hom.: 392 Cov.: 33

Gnomad AFR AF: 0.0344

Gnomad AMI AF: 0.0406

Gnomad AMR AF: 0.0762

Gnomad ASJ AF: 0.0493

Gnomad EAS AF: 0.0943

Gnomad SAS AF: 0.0661

Gnomad FIN AF: 0.0721

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.0869

Gnomad OTH AF: 0.0922

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

GnomAD4 genome AF: 0.0689 AC: 10495 AN: 152244 Hom.: 391 Cov.: 33 AF XY: 0.0690 AC XY: 5136 AN XY: 74422

Gnomad4 AFR AF: 0.0345

Gnomad4 AMR AF: 0.0761

Gnomad4 ASJ AF: 0.0493

Gnomad4 EAS AF: 0.0945

Gnomad4 SAS AF: 0.0653

Gnomad4 FIN AF: 0.0721

Gnomad4 NFE AF: 0.0869

Gnomad4 OTH AF: 0.0912

Alfa AF: 0.0723 Hom.: 62

Bravo AF: 0.0686

Asia WGS AF: 0.0630 AC: 219 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	0.88
Dann	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs728142; hg19: chr10-44889459;