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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107987122	XR_001746919.2	n.453-2325A>G		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000297691	ENST00000750211.1	n.102-2325A>G		intron_variant	Intron 1 of 7
ENSG00000297691	ENST00000750212.1	n.184-2325A>G		intron_variant	Intron 1 of 3
ENSG00000297691	ENST00000750213.1	n.121-2325A>G		intron_variant	Intron 1 of 1

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 v4.3

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

Other links and lift over

dbSNP: rs7859491; hg19: chr9-122639288; COSMIC: COSV60400101;