rs2726566

chr8-58747717-G-A

Variant summary

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

The XR_928924.3(LOC105375858):n.190+757C>T 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 0.0491 in 152,096 control chromosomes in the GnomAD database, including 251 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 0.049 (251 hom., cov: 32)
• Consequence: LOC105375858 XR_928924.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.11

Genes affected

LOC105375858 (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 = 0.126 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105375858	XR_928924.3	n.190+757C>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0491 AC: 7457 AN: 151978 Hom.: 250 Cov.: 32

Gnomad AFR AF: 0.0202

Gnomad AMI AF: 0.0473

Gnomad AMR AF: 0.0876

Gnomad ASJ AF: 0.0677

Gnomad EAS AF: 0.135

Gnomad SAS AF: 0.0406

Gnomad FIN AF: 0.0205

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.0553

Gnomad OTH AF: 0.0584

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

GnomAD4 genome AF: 0.0491 AC: 7469 AN: 152096 Hom.: 251 Cov.: 32 AF XY: 0.0494 AC XY: 3676 AN XY: 74368

Gnomad4 AFR AF: 0.0202

Gnomad4 AMR AF: 0.0879

Gnomad4 ASJ AF: 0.0677

Gnomad4 EAS AF: 0.135

Gnomad4 SAS AF: 0.0407

Gnomad4 FIN AF: 0.0205

Gnomad4 NFE AF: 0.0553

Gnomad4 OTH AF: 0.0592

Alfa AF: 0.0500 Hom.: 32

Bravo AF: 0.0548

Asia WGS AF: 0.101 AC: 355 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	1.0
Dann	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2726566; hg19: chr8-59660276;