6-90902207-G-T

Variant names:

• chr6-90902207-G-T
• rs12191179
• ENST00000828793.1:n.176-5849G>T

Variant summary

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

The ENST00000828793.1(ENSG00000307789):​n.176-5849G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.188 in 152,064 control chromosomes in the GnomAD database, including 2,877 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 0.19 (2877 hom., cov: 32)
• Consequence: ENSG00000307789 ENST00000828793.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.366
• Publications: 2 publications found

Genes affected

ENSG00000307789 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.251 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107986623	XR_001744259.1	n.1244-5849G>T		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000307789	ENST00000828793.1	n.176-5849G>T		intron_variant	Intron 1 of 3
ENSG00000307789	ENST00000828794.1	n.411-5849G>T		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.188 AC: 28567 AN: 151946 Hom.: 2870 Cov.: 32

Gnomad AFR AF: 0.255

Gnomad AMI AF: 0.0969

Gnomad AMR AF: 0.195

Gnomad ASJ AF: 0.176

Gnomad EAS AF: 0.0350

Gnomad SAS AF: 0.150

Gnomad FIN AF: 0.187

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.162

Gnomad OTH AF: 0.168

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

GnomAD4 genome AF: 0.188 AC: 28611 AN: 152064 Hom.: 2877 Cov.: 32 AF XY: 0.187 AC XY: 13930 AN XY: 74318

African (AFR) AF: 0.255 AC: 10596 AN: 41494

American (AMR) AF: 0.196 AC: 2988 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.176 AC: 609 AN: 3470

East Asian (EAS) AF: 0.0349 AC: 180 AN: 5162

South Asian (SAS) AF: 0.150 AC: 720 AN: 4816

European-Finnish (FIN) AF: 0.187 AC: 1980 AN: 10564

Middle Eastern (MID) AF: 0.262 AC: 77 AN: 294

European-Non Finnish (NFE) AF: 0.162 AC: 11019 AN: 67964

Other (OTH) AF: 0.168 AC: 354 AN: 2110

Alfa AF: 0.166 Hom.: 9184

Bravo AF: 0.190

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.77
DANN	Benign	0.52
PhyloP100		-0.37

Splicing

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

Other links and lift over

dbSNP: rs12191179; hg19: chr6-91611925;