rs2928445

chr10-57387016-T-Cchr10-57387016-T-G

Variant summary

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

The XR_001747453.1(LOC105378313):n.63-10910A>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 0.219 in 151,904 control chromosomes in the GnomAD database, including 5,979 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 0.22 (5979 hom., cov: 29)
• Consequence: LOC105378313 XR_001747453.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.930

Genes affected

LOC105378313 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.476 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105378313	XR_001747453.1	n.63-10910A>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.219 AC: 33221 AN: 151786 Hom.: 5972 Cov.: 29

Gnomad AFR AF: 0.482

Gnomad AMI AF: 0.0219

Gnomad AMR AF: 0.262

Gnomad ASJ AF: 0.0836

Gnomad EAS AF: 0.227

Gnomad SAS AF: 0.236

Gnomad FIN AF: 0.0643

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.0828

Gnomad OTH AF: 0.191

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

GnomAD4 genome AF: 0.219 AC: 33273 AN: 151904 Hom.: 5979 Cov.: 29 AF XY: 0.220 AC XY: 16371 AN XY: 74252

Gnomad4 AFR AF: 0.482

Gnomad4 AMR AF: 0.262

Gnomad4 ASJ AF: 0.0836

Gnomad4 EAS AF: 0.227

Gnomad4 SAS AF: 0.234

Gnomad4 FIN AF: 0.0643

Gnomad4 NFE AF: 0.0828

Gnomad4 OTH AF: 0.192

Alfa AF: 0.115 Hom.: 1640

Bravo AF: 0.245

Asia WGS AF: 0.266 AC: 926 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	0.38
Dann	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2928445; hg19: chr10-59146776;