rs12125058

Variant names:

• chr1-221104166-C-T
• rs12125058
• ENST00000739959.1:n.95-867C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000739959.1(ENSG00000296502):​n.95-867C>T variant causes a intron 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: ENSG00000296502 ENST00000739959.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.442
• Publications: 6 publications found

Genes affected

ENSG00000296502 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LOC101929750	XR_001738477.2	n.1024-867C>T		intron_variant	Intron 7 of 8
LOC101929750	XR_001738478.2	n.733-549C>T		intron_variant	Intron 5 of 7
LOC101929750	XR_001738479.2	n.733-867C>T		intron_variant	Intron 5 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000296502	ENST00000739959.1	n.95-867C>T		intron_variant	Intron 1 of 2
ENSG00000296502	ENST00000739960.1	n.95-549C>T		intron_variant	Intron 1 of 4

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

African (AFR) AF: 0.414 AC: 17164 AN: 41414

American (AMR) AF: 0.448 AC: 6844 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.542 AC: 1881 AN: 3468

East Asian (EAS) AF: 0.404 AC: 2086 AN: 5160

South Asian (SAS) AF: 0.390 AC: 1875 AN: 4812

European-Finnish (FIN) AF: 0.547 AC: 5767 AN: 10548

Middle Eastern (MID) AF: 0.701 AC: 206 AN: 294

European-Non Finnish (NFE) AF: 0.585 AC: 39748 AN: 67938

Other (OTH) AF: 0.542 AC: 1142 AN: 2108

Alfa AF: 0.550 Hom.: 9181

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
PhyloP100		-0.44

Splicing

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

Other links and lift over

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