8-92412393-T-G

Variant names:

• chr8-92412393-T-G
• rs9297909
• ENST00000518042.2:n.265+988A>C

Variant summary

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

The ENST00000518042.2(ENSG00000253682):​n.265+988A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.494 in 151,922 control chromosomes in the GnomAD database, including 19,599 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 0.49 (19599 hom., cov: 32)
• Consequence: ENSG00000253682 ENST00000518042.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.186
• Publications: 1 publications found

Genes affected

ENSG00000253682 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.715 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000518042.2. 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
	LOC105375638	NR_188050.1		n.82+988A>C		intron	N/A
	LOC105375638	NR_188051.1		n.82+988A>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000253682	ENST00000518042.2	TSL:3	n.265+988A>C		intron	N/A
	ENSG00000253682	ENST00000655386.1		n.270+988A>C		intron	N/A
	ENSG00000253682	ENST00000659155.2		n.301+988A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.494 AC: 74967 AN: 151804 Hom.: 19585 Cov.: 32

Gnomad AFR AF: 0.324

Gnomad AMI AF: 0.610

Gnomad AMR AF: 0.582

Gnomad ASJ AF: 0.544

Gnomad EAS AF: 0.734

Gnomad SAS AF: 0.701

Gnomad FIN AF: 0.596

Gnomad MID AF: 0.532

Gnomad NFE AF: 0.525

Gnomad OTH AF: 0.472

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

GnomAD4 genome AF: 0.494 AC: 75022 AN: 151922 Hom.: 19599 Cov.: 32 AF XY: 0.503 AC XY: 37357 AN XY: 74230

African (AFR) AF: 0.324 AC: 13427 AN: 41434

American (AMR) AF: 0.583 AC: 8889 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.544 AC: 1887 AN: 3470

East Asian (EAS) AF: 0.734 AC: 3785 AN: 5156

South Asian (SAS) AF: 0.701 AC: 3372 AN: 4808

European-Finnish (FIN) AF: 0.596 AC: 6280 AN: 10534

Middle Eastern (MID) AF: 0.531 AC: 155 AN: 292

European-Non Finnish (NFE) AF: 0.525 AC: 35673 AN: 67962

Other (OTH) AF: 0.476 AC: 998 AN: 2096

Alfa AF: 0.515 Hom.: 62072

Bravo AF: 0.481

Asia WGS AF: 0.706 AC: 2452 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	3.0
DANN	Benign	0.83
PhyloP100		-0.19

Splicing

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

Other links and lift over

dbSNP: rs9297909; hg19: chr8-93424621;