rs9390537

Variant names:

• chr6-148102235-C-T
• rs9390537
• ENST00000720858.1:n.49+1345G>A

Variant summary

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

The ENST00000720858.1(ENSG00000294086):​n.49+1345G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.724 in 151,828 control chromosomes in the GnomAD database, including 40,804 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 0.72 (40804 hom., cov: 29)
• Consequence: ENSG00000294086 ENST00000720858.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.196
• Publications: 12 publications found

Genes affected

ENSG00000294086 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.793 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000720858.1. 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
	ENSG00000294086	ENST00000720858.1		n.49+1345G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.724 AC: 109827 AN: 151712 Hom.: 40785 Cov.: 29

Gnomad AFR AF: 0.708

Gnomad AMI AF: 0.768

Gnomad AMR AF: 0.568

Gnomad ASJ AF: 0.733

Gnomad EAS AF: 0.339

Gnomad SAS AF: 0.520

Gnomad FIN AF: 0.798

Gnomad MID AF: 0.788

Gnomad NFE AF: 0.799

Gnomad OTH AF: 0.727

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

GnomAD4 genome AF: 0.724 AC: 109886 AN: 151828 Hom.: 40804 Cov.: 29 AF XY: 0.713 AC XY: 52935 AN XY: 74194

African (AFR) AF: 0.708 AC: 29303 AN: 41388

American (AMR) AF: 0.567 AC: 8640 AN: 15234

Ashkenazi Jewish (ASJ) AF: 0.733 AC: 2542 AN: 3468

East Asian (EAS) AF: 0.340 AC: 1743 AN: 5124

South Asian (SAS) AF: 0.520 AC: 2494 AN: 4792

European-Finnish (FIN) AF: 0.798 AC: 8420 AN: 10548

Middle Eastern (MID) AF: 0.796 AC: 234 AN: 294

European-Non Finnish (NFE) AF: 0.799 AC: 54287 AN: 67954

Other (OTH) AF: 0.720 AC: 1523 AN: 2114

Alfa AF: 0.757 Hom.: 115837

Bravo AF: 0.704

Asia WGS AF: 0.403 AC: 1407 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	3.9
DANN	Benign	0.55
PhyloP100		0.20

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: rs9390537;

hg19: chr6-148423371;