chr1-146037054-T-A

Variant names:

• chr1-146037054-T-A
• rs7536827
• unassigned_transcript_156:c.-7T>A

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000000000(TRG-TCC2-1):​c.-7T>A variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.432 in 152,082 control chromosomes in the GnomAD database, including 14,558 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 0.43 (14558 hom., cov: 32)
• Consequence: TRG-TCC2-1 ENST00000000000 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.79
• Publications: 10 publications found

Genes affected

TRG-TCC2-1 (HGNC:34623):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.46).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.478 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.432 AC: 65711 AN: 151964 Hom.: 14557 Cov.: 32

Gnomad AFR AF: 0.361

Gnomad AMI AF: 0.354

Gnomad AMR AF: 0.385

Gnomad ASJ AF: 0.437

Gnomad EAS AF: 0.438

Gnomad SAS AF: 0.495

Gnomad FIN AF: 0.485

Gnomad MID AF: 0.421

Gnomad NFE AF: 0.475

Gnomad OTH AF: 0.409

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

GnomAD4 genome AF: 0.432 AC: 65738 AN: 152082 Hom.: 14558 Cov.: 32 AF XY: 0.434 AC XY: 32280 AN XY: 74336

African (AFR) AF: 0.360 AC: 14943 AN: 41492

American (AMR) AF: 0.384 AC: 5864 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.437 AC: 1511 AN: 3460

East Asian (EAS) AF: 0.439 AC: 2275 AN: 5182

South Asian (SAS) AF: 0.495 AC: 2390 AN: 4828

European-Finnish (FIN) AF: 0.485 AC: 5125 AN: 10566

Middle Eastern (MID) AF: 0.422 AC: 124 AN: 294

European-Non Finnish (NFE) AF: 0.475 AC: 32319 AN: 67982

Other (OTH) AF: 0.411 AC: 866 AN: 2106

Alfa AF: 0.311 Hom.: 812

Bravo AF: 0.417

Asia WGS AF: 0.456 AC: 1584 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.46
CADD	Benign	0.0010
DANN	Benign	0.33
PhyloP100		-3.8
PromoterAI		0.0050	Neutral

Splicing

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

Other links and lift over

dbSNP: rs7536827; hg19: chr1-145397942;