chr1-146037049-C-T

Variant names:

• chr1-146037049-C-T
• rs7536830
• unassigned_transcript_156:c.-12C>T

Variant summary

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

The ENST00000000000(TRG-TCC2-1):​c.-12C>T variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.298 in 152,086 control chromosomes in the GnomAD database, including 7,768 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 0.30 (7768 hom., cov: 32)
• Consequence: TRG-TCC2-1 ENST00000000000 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -12.3
• Publications: 11 publications found

Genes affected

TRG-TCC2-1 (HGNC:34623):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.47).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.375 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.298 AC: 45293 AN: 151968 Hom.: 7769 Cov.: 32

Gnomad AFR AF: 0.140

Gnomad AMI AF: 0.463

Gnomad AMR AF: 0.347

Gnomad ASJ AF: 0.308

Gnomad EAS AF: 0.169

Gnomad SAS AF: 0.244

Gnomad FIN AF: 0.390

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.379

Gnomad OTH AF: 0.329

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

GnomAD4 genome AF: 0.298 AC: 45304 AN: 152086 Hom.: 7768 Cov.: 32 AF XY: 0.296 AC XY: 21977 AN XY: 74342

African (AFR) AF: 0.140 AC: 5819 AN: 41498

American (AMR) AF: 0.347 AC: 5292 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.308 AC: 1066 AN: 3464

East Asian (EAS) AF: 0.169 AC: 876 AN: 5192

South Asian (SAS) AF: 0.244 AC: 1177 AN: 4822

European-Finnish (FIN) AF: 0.390 AC: 4123 AN: 10568

Middle Eastern (MID) AF: 0.241 AC: 71 AN: 294

European-Non Finnish (NFE) AF: 0.379 AC: 25774 AN: 67970

Other (OTH) AF: 0.326 AC: 685 AN: 2104

Alfa AF: 0.326 Hom.: 6305

Bravo AF: 0.292

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.47
CADD	Benign	0.0010
PhyloP100		-12
PromoterAI		-0.043	Neutral

Splicing

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

Other links and lift over

dbSNP: rs7536830; hg19: chr1-145397947;