rs926300

Variant names:

• chr6-27091664-A-T
• rs926300
• unassigned_transcript_992:c.-78A>T

Variant summary

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

The ENST00000000000(TRP-CGG2-1):​c.-78A>T variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.138 in 152,104 control chromosomes in the GnomAD database, including 1,596 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 0.14 (1596 hom., cov: 31)
• Consequence: TRP-CGG2-1 ENST00000000000 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0590
• Publications: 20 publications found

Genes affected

TRP-CGG2-1 (HGNC:34734):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.45).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.167 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: 0.139 AC: 21057 AN: 151986 Hom.: 1596 Cov.: 31

Gnomad AFR AF: 0.138

Gnomad AMI AF: 0.213

Gnomad AMR AF: 0.106

Gnomad ASJ AF: 0.0789

Gnomad EAS AF: 0.00884

Gnomad SAS AF: 0.0940

Gnomad FIN AF: 0.0894

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.170

Gnomad OTH AF: 0.124

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

GnomAD4 genome AF: 0.138 AC: 21058 AN: 152104 Hom.: 1596 Cov.: 31 AF XY: 0.132 AC XY: 9813 AN XY: 74376

African (AFR) AF: 0.138 AC: 5707 AN: 41464

American (AMR) AF: 0.105 AC: 1611 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.0789 AC: 274 AN: 3472

East Asian (EAS) AF: 0.00886 AC: 46 AN: 5194

South Asian (SAS) AF: 0.0926 AC: 447 AN: 4826

European-Finnish (FIN) AF: 0.0894 AC: 945 AN: 10570

Middle Eastern (MID) AF: 0.136 AC: 40 AN: 294

European-Non Finnish (NFE) AF: 0.170 AC: 11535 AN: 67982

Other (OTH) AF: 0.123 AC: 259 AN: 2112

Alfa AF: 0.151 Hom.: 225

Bravo AF: 0.140

Asia WGS AF: 0.0600 AC: 208 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.45
CADD	Benign	3.7
DANN	Benign	0.53
PhyloP100		0.059

Splicing

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

Other links and lift over

dbSNP: rs926300; hg19: chr6-27059443;