chr6-90902207-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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000828793.1. You can select a different transcript below to see updated ACMG assignments.

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
	ENSG00000307789	ENST00000828793.1		n.176-5849G>T		intron	N/A
	ENSG00000307789	ENST00000828794.1		n.411-5849G>T		intron	N/A

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 v4.9

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;