rs675597

Variant names:

• chr9-87937727-A-G
• rs675597
• ENST00000783884.1:n.19T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000783884.1(ENSG00000289459):​n.19T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. 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 0.013 (410 hom., cov: 17)
• Consequence: ENSG00000289459 ENST00000783884.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.89
• Publications: 1 publications found

Genes affected

ENSG00000289459 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BS1: Variant frequency is greater than expected in population afr. GnomAd4 allele frequency = 0.0131 (1482/113284) while in subpopulation AFR AF = 0.0443 (1377/31088). AF 95% confidence interval is 0.0423. There are 410 homozygotes in GnomAd4. There are 680 alleles in the male GnomAd4 subpopulation. Median coverage is 17. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 410 gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000783884.1. 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
	LOC497256	NR_149022.1		n.362+1172T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000289459	ENST00000783884.1		n.19T>C		non_coding_transcript_exon	Exon 1 of 4
	ENSG00000289459	ENST00000685869.2		n.376+1168T>C		intron	N/A
	ENSG00000289459	ENST00000783876.1		n.237+1168T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0131 AC: 1482 AN: 113212 Hom.: 411 Cov.: 17

Gnomad AFR AF: 0.0444

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00326

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00272

Gnomad SAS AF: 0.00123

Gnomad FIN AF: 0.000258

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000570

Gnomad OTH AF: 0.0116

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

GnomAD4 genome AF: 0.0131 AC: 1482 AN: 113284 Hom.: 410 Cov.: 17 AF XY: 0.0123 AC XY: 680 AN XY: 55446

African (AFR) AF: 0.0443 AC: 1377 AN: 31088

American (AMR) AF: 0.00326 AC: 40 AN: 12286

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2476

East Asian (EAS) AF: 0.00273 AC: 13 AN: 4766

South Asian (SAS) AF: 0.00123 AC: 4 AN: 3240

European-Finnish (FIN) AF: 0.000258 AC: 2 AN: 7766

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 194

European-Non Finnish (NFE) AF: 0.000570 AC: 28 AN: 49148

Other (OTH) AF: 0.0115 AC: 18 AN: 1568

Alfa AF: 0.0111 Hom.: 35

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.2
DANN	Benign	0.88
PhyloP100		-1.9

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: rs675597;

hg19: chr9-90552642;