ENST00000797726.1:n.65+186T>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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC102724234	XR_427872.3	n.60+186T>G		intron_variant	Intron 1 of 2
LOC102724234	XR_926434.2	n.60+186T>G		intron_variant	Intron 1 of 2
LOC102724234	XR_926435.2	n.60+186T>G		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000303868	ENST00000797726.1	n.65+186T>G		intron_variant	Intron 1 of 4
ENSG00000303868	ENST00000797727.1	n.64+186T>G		intron_variant	Intron 1 of 2
ENSG00000303868	ENST00000797728.1	n.63+186T>G		intron_variant	Intron 1 of 4

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 v4.3

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

Other links and lift over

dbSNP: rs9392158; hg19: chr6-7427350;