rs1558324

Positions:

• chr12-6180053-G-A
• chr12-6180053-G-C

Variant summary

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

The XR_931588.3(LOC105369623):​n.433+546C>T 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 0.487 in 151,972 control chromosomes in the GnomAD database, including 19,665 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 0.49 (19665 hom., cov: 32)
• Consequence: LOC105369623 XR_931588.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0190

Genes affected

LOC105369623 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.715 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105369623	XR_931588.3	n.433+546C>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.486 AC: 73857 AN: 151854 Hom.: 19629 Cov.: 32

Gnomad AFR AF: 0.721

Gnomad AMI AF: 0.496

Gnomad AMR AF: 0.336

Gnomad ASJ AF: 0.287

Gnomad EAS AF: 0.413

Gnomad SAS AF: 0.405

Gnomad FIN AF: 0.372

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.419

Gnomad OTH AF: 0.424

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

GnomAD4 genome AF: 0.487 AC: 73944 AN: 151972 Hom.: 19665 Cov.: 32 AF XY: 0.479 AC XY: 35613 AN XY: 74272

Gnomad4 AFR AF: 0.722

Gnomad4 AMR AF: 0.335

Gnomad4 ASJ AF: 0.287

Gnomad4 EAS AF: 0.413

Gnomad4 SAS AF: 0.405

Gnomad4 FIN AF: 0.372

Gnomad4 NFE AF: 0.419

Gnomad4 OTH AF: 0.425

Alfa AF: 0.423 Hom.: 13674

Bravo AF: 0.492

Asia WGS AF: 0.417 AC: 1451 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.22
DANN	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1558324; hg19: chr12-6289219;