rs10548381

chr12-27331677-TCTA-Tchr12-27331677-TCTA-TCTACTA

Variant summary

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

The XR_007063255.1(LOC124902906):n.176+942_176+944del 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 0.078 in 152,252 control chromosomes in the GnomAD database, including 517 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.078 (517 hom., cov: 30)
• Consequence: LOC124902906 XR_007063255.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.519

Genes affected

LOC124902906 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.103 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124902906	XR_007063255.1	n.176+942_176+944del		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0781 AC: 11876 AN: 152134 Hom.: 517 Cov.: 30

Gnomad AFR AF: 0.0426

Gnomad AMI AF: 0.156

Gnomad AMR AF: 0.0535

Gnomad ASJ AF: 0.0766

Gnomad EAS AF: 0.0406

Gnomad SAS AF: 0.0491

Gnomad FIN AF: 0.105

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.105

Gnomad OTH AF: 0.0651

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

GnomAD4 genome AF: 0.0780 AC: 11876 AN: 152252 Hom.: 517 Cov.: 30 AF XY: 0.0773 AC XY: 5754 AN XY: 74448

Gnomad4 AFR AF: 0.0425

Gnomad4 AMR AF: 0.0534

Gnomad4 ASJ AF: 0.0766

Gnomad4 EAS AF: 0.0407

Gnomad4 SAS AF: 0.0491

Gnomad4 FIN AF: 0.105

Gnomad4 NFE AF: 0.105

Gnomad4 OTH AF: 0.0649

Alfa AF: 0.103 Hom.: 110

Bravo AF: 0.0710

Asia WGS AF: 0.0450 AC: 156 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: rs10548381; hg19: chr12-27484610;