rs7859491

Variant names:

• chr9-119877010-T-C
• rs7859491
• ENST00000750211.1:n.102-2325A>G

Variant summary

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

The ENST00000750211.1(ENSG00000297691):​n.102-2325A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.256 in 151,952 control chromosomes in the GnomAD database, including 10,086 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 0.26 (10086 hom., cov: 32)
• Consequence: ENSG00000297691 ENST00000750211.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.465
• Publications: 2 publications found

Genes affected

ENSG00000297691 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.663 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000750211.1. 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
	ENSG00000297691	ENST00000750211.1		n.102-2325A>G		intron	N/A
	ENSG00000297691	ENST00000750212.1		n.184-2325A>G		intron	N/A
	ENSG00000297691	ENST00000750213.1		n.121-2325A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.256 AC: 38824 AN: 151834 Hom.: 10042 Cov.: 32

Gnomad AFR AF: 0.669

Gnomad AMI AF: 0.116

Gnomad AMR AF: 0.157

Gnomad ASJ AF: 0.0559

Gnomad EAS AF: 0.00270

Gnomad SAS AF: 0.0245

Gnomad FIN AF: 0.0671

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.107

Gnomad OTH AF: 0.207

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

GnomAD4 genome AF: 0.256 AC: 38928 AN: 151952 Hom.: 10086 Cov.: 32 AF XY: 0.246 AC XY: 18259 AN XY: 74304

African (AFR) AF: 0.669 AC: 27682 AN: 41360

American (AMR) AF: 0.157 AC: 2398 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.0559 AC: 194 AN: 3470

East Asian (EAS) AF: 0.00271 AC: 14 AN: 5172

South Asian (SAS) AF: 0.0245 AC: 118 AN: 4822

European-Finnish (FIN) AF: 0.0671 AC: 710 AN: 10582

Middle Eastern (MID) AF: 0.0918 AC: 27 AN: 294

European-Non Finnish (NFE) AF: 0.107 AC: 7240 AN: 67976

Other (OTH) AF: 0.208 AC: 439 AN: 2112

Alfa AF: 0.254 Hom.: 1788

Bravo AF: 0.283

Asia WGS AF: 0.0700 AC: 246 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.0
DANN	Benign	0.42
PhyloP100		-0.47

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: rs7859491;

hg19: chr9-122639288;

COSMIC: COSV60400101;