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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TRP-CGG2-1	unassigned_transcript_992	c.-78A>T		upstream_gene_variant

Ensembl

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

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 v4.3

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;