10-58451030-T-G

Variant summary

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

The XR_945981.3(LOC105378316):n.360+15373T>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 0.613 in 152,018 control chromosomes in the GnomAD database, including 31,618 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 0.61 (31618 hom., cov: 32)
• Consequence: LOC105378316 XR_945981.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.100

Genes affected

LOC105378316 (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 (NFE) allele frequency at 95% confidence interval = 0.756 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105378316	XR_945981.3	n.360+15373T>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.613 AC: 93159 AN: 151900 Hom.: 31615 Cov.: 32

Gnomad AFR AF: 0.297

Gnomad AMI AF: 0.758

Gnomad AMR AF: 0.725

Gnomad ASJ AF: 0.690

Gnomad EAS AF: 0.660

Gnomad SAS AF: 0.561

Gnomad FIN AF: 0.699

Gnomad MID AF: 0.639

Gnomad NFE AF: 0.761

Gnomad OTH AF: 0.625

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

GnomAD4 genome AF: 0.613 AC: 93178 AN: 152018 Hom.: 31618 Cov.: 32 AF XY: 0.613 AC XY: 45500 AN XY: 74260

Gnomad4 AFR AF: 0.297

Gnomad4 AMR AF: 0.725

Gnomad4 ASJ AF: 0.690

Gnomad4 EAS AF: 0.661

Gnomad4 SAS AF: 0.560

Gnomad4 FIN AF: 0.699

Gnomad4 NFE AF: 0.761

Gnomad4 OTH AF: 0.620

Alfa AF: 0.661 Hom.: 4938

Bravo AF: 0.606

Asia WGS AF: 0.559 AC: 1936 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	3.1
Dann	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10509091; hg19: chr10-60210790;