rs7536827

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr1-146037054-T-A
• chr1-146037054-T-C
• chr1-146037054-T-G

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

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 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.79

Genes affected

TRG-TCC2-1 (HGNC:34623):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TRG-TCC2-1	unassigned_transcript_156	c.-7T>A		upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.360

Gnomad4 AMR AF: 0.384

Gnomad4 ASJ AF: 0.437

Gnomad4 EAS AF: 0.439

Gnomad4 SAS AF: 0.495

Gnomad4 FIN AF: 0.485

Gnomad4 NFE AF: 0.475

Gnomad4 OTH AF: 0.411

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.46
CADD	Benign	0.0010
DANN	Benign	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7536827; hg19: chr1-145397942;