10-32007305-CTG-C

Position:

• chr10-32007305-CTG-C

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The XR_001747415.2(LOC107984219):​n.5354-10717_5354-10716del variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.47 (17242 hom., cov: 0)
• Consequence: LOC107984219 XR_001747415.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0580

Genes affected

LOC107984219 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.588 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC107984219	XR_001747415.2	n.5354-10717_5354-10716del		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.470 AC: 71056 AN: 151290 Hom.: 17242 Cov.: 0

Gnomad AFR AF: 0.350

Gnomad AMI AF: 0.540

Gnomad AMR AF: 0.478

Gnomad ASJ AF: 0.472

Gnomad EAS AF: 0.605

Gnomad SAS AF: 0.493

Gnomad FIN AF: 0.595

Gnomad MID AF: 0.462

Gnomad NFE AF: 0.508

Gnomad OTH AF: 0.470

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

GnomAD4 genome AF: 0.469 AC: 71079 AN: 151408 Hom.: 17242 Cov.: 0 AF XY: 0.474 AC XY: 35046 AN XY: 73930

Gnomad4 AFR AF: 0.350

Gnomad4 AMR AF: 0.477

Gnomad4 ASJ AF: 0.472

Gnomad4 EAS AF: 0.605

Gnomad4 SAS AF: 0.495

Gnomad4 FIN AF: 0.595

Gnomad4 NFE AF: 0.508

Gnomad4 OTH AF: 0.468

Alfa AF: 0.492 Hom.: 2269

Bravo AF: 0.456

Asia WGS AF: 0.516 AC: 1790 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4016810; hg19: chr10-32296233;