6-7427117-T-G

Variant names:

• chr6-7427117-T-G
• rs9392158
• ENST00000797726.1:n.65+186T>G

Variant summary

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

The ENST00000797726.1(ENSG00000303868):​n.65+186T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.107 in 152,162 control chromosomes in the GnomAD database, including 1,210 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 0.11 (1210 hom., cov: 33)
• Consequence: ENSG00000303868 ENST00000797726.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.147
• Publications: 3 publications found

Genes affected

ENSG00000303868 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.305 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000797726.1. You can select a different transcript below to see updated ACMG assignments.

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
	ENSG00000303868	ENST00000797726.1		n.65+186T>G		intron	N/A
	ENSG00000303868	ENST00000797727.1		n.64+186T>G		intron	N/A
	ENSG00000303868	ENST00000797728.1		n.63+186T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.107 AC: 16239 AN: 152044 Hom.: 1209 Cov.: 33

Gnomad AFR AF: 0.0492

Gnomad AMI AF: 0.148

Gnomad AMR AF: 0.212

Gnomad ASJ AF: 0.114

Gnomad EAS AF: 0.318

Gnomad SAS AF: 0.138

Gnomad FIN AF: 0.124

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.0961

Gnomad OTH AF: 0.116

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

GnomAD4 genome AF: 0.107 AC: 16241 AN: 152162 Hom.: 1210 Cov.: 33 AF XY: 0.113 AC XY: 8401 AN XY: 74376

African (AFR) AF: 0.0492 AC: 2044 AN: 41528

American (AMR) AF: 0.211 AC: 3225 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.114 AC: 396 AN: 3468

East Asian (EAS) AF: 0.318 AC: 1645 AN: 5170

South Asian (SAS) AF: 0.138 AC: 666 AN: 4818

European-Finnish (FIN) AF: 0.124 AC: 1312 AN: 10592

Middle Eastern (MID) AF: 0.129 AC: 38 AN: 294

European-Non Finnish (NFE) AF: 0.0961 AC: 6536 AN: 68008

Other (OTH) AF: 0.116 AC: 244 AN: 2112

Alfa AF: 0.105 Hom.: 180

Bravo AF: 0.109

Asia WGS AF: 0.202 AC: 702 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.3
DANN	Benign	0.084
PhyloP100		0.15

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs9392158;

hg19: chr6-7427350;