rs1325586

chr10-3281581-T-C

Variant summary

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

The XR_001747320.2(LOC107987146):n.378-462T>C 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 0.6 in 152,142 control chromosomes in the GnomAD database, including 27,568 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 0.60 (27568 hom., cov: 34)
• Consequence: LOC107987146 XR_001747320.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.572

Genes affected

LOC107987146 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.71 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107987146	XR_001747320.2	n.378-462T>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.600 AC: 91154 AN: 152024 Hom.: 27552 Cov.: 34

Gnomad AFR AF: 0.575

Gnomad AMI AF: 0.605

Gnomad AMR AF: 0.698

Gnomad ASJ AF: 0.468

Gnomad EAS AF: 0.504

Gnomad SAS AF: 0.730

Gnomad FIN AF: 0.600

Gnomad MID AF: 0.510

Gnomad NFE AF: 0.597

Gnomad OTH AF: 0.602

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

GnomAD4 genome AF: 0.600 AC: 91210 AN: 152142 Hom.: 27568 Cov.: 34 AF XY: 0.603 AC XY: 44885 AN XY: 74382

Gnomad4 AFR AF: 0.574

Gnomad4 AMR AF: 0.698

Gnomad4 ASJ AF: 0.468

Gnomad4 EAS AF: 0.505

Gnomad4 SAS AF: 0.731

Gnomad4 FIN AF: 0.600

Gnomad4 NFE AF: 0.597

Gnomad4 OTH AF: 0.602

Alfa AF: 0.594 Hom.: 25431

Bravo AF: 0.602

Asia WGS AF: 0.622 AC: 2161 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	4.2
Dann	Benign	0.29

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1325586; hg19: chr10-3323773;