rs12125058

chr1-221104166-C-T

Variant summary

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

The XR_001738477.2(LOC101929750):n.1024-867C>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 0.507 in 151,934 control chromosomes in the GnomAD database, including 20,218 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 0.51 (20218 hom., cov: 31)
• Consequence: LOC101929750 XR_001738477.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.442

Genes affected

LOC101929750 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.58 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC101929750	XR_001738477.2	n.1024-867C>T		intron_variant, non_coding_transcript_variant
LOC101929750	XR_001738478.2	n.733-549C>T		intron_variant, non_coding_transcript_variant
LOC101929750	XR_001738479.2	n.733-867C>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.507 AC: 77028 AN: 151816 Hom.: 20206 Cov.: 31

Gnomad AFR AF: 0.415

Gnomad AMI AF: 0.379

Gnomad AMR AF: 0.449

Gnomad ASJ AF: 0.542

Gnomad EAS AF: 0.405

Gnomad SAS AF: 0.388

Gnomad FIN AF: 0.547

Gnomad MID AF: 0.684

Gnomad NFE AF: 0.585

Gnomad OTH AF: 0.541

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

GnomAD4 genome AF: 0.507 AC: 77058 AN: 151934 Hom.: 20218 Cov.: 31 AF XY: 0.502 AC XY: 37278 AN XY: 74270

Gnomad4 AFR AF: 0.414

Gnomad4 AMR AF: 0.448

Gnomad4 ASJ AF: 0.542

Gnomad4 EAS AF: 0.404

Gnomad4 SAS AF: 0.390

Gnomad4 FIN AF: 0.547

Gnomad4 NFE AF: 0.585

Gnomad4 OTH AF: 0.542

Alfa AF: 0.545 Hom.: 5806

Bravo AF: 0.497

Asia WGS AF: 0.393 AC: 1366 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	0.79
Dann	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12125058; hg19: chr1-221277508; COSMIC: COSV60030390;