rs7023003

Variant names:

• chr9-105118389-A-G
• rs7023003
• ENST00000666856.1:n.1857+49231T>C

Variant summary

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

The ENST00000666856.1(ENSG00000286536):​n.1857+49231T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.28 in 151,742 control chromosomes in the GnomAD database, including 7,079 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 0.28 (7079 hom., cov: 31)
• Consequence: ENSG00000286536 ENST00000666856.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.15
• Publications: 4 publications found

Genes affected

ENSG00000286536 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.467 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000666856.1. 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
	ENSG00000286536	ENST00000666856.1		n.1857+49231T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.280 AC: 42392 AN: 151626 Hom.: 7050 Cov.: 31

Gnomad AFR AF: 0.472

Gnomad AMI AF: 0.134

Gnomad AMR AF: 0.190

Gnomad ASJ AF: 0.207

Gnomad EAS AF: 0.313

Gnomad SAS AF: 0.191

Gnomad FIN AF: 0.221

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.203

Gnomad OTH AF: 0.263

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

GnomAD4 genome AF: 0.280 AC: 42469 AN: 151742 Hom.: 7079 Cov.: 31 AF XY: 0.278 AC XY: 20585 AN XY: 74150

African (AFR) AF: 0.472 AC: 19468 AN: 41230

American (AMR) AF: 0.190 AC: 2887 AN: 15224

Ashkenazi Jewish (ASJ) AF: 0.207 AC: 719 AN: 3472

East Asian (EAS) AF: 0.313 AC: 1618 AN: 5162

South Asian (SAS) AF: 0.192 AC: 925 AN: 4822

European-Finnish (FIN) AF: 0.221 AC: 2325 AN: 10534

Middle Eastern (MID) AF: 0.262 AC: 77 AN: 294

European-Non Finnish (NFE) AF: 0.203 AC: 13776 AN: 67980

Other (OTH) AF: 0.261 AC: 552 AN: 2112

Alfa AF: 0.245 Hom.: 969

Bravo AF: 0.289

Asia WGS AF: 0.266 AC: 923 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.79
DANN	Benign	0.50
PhyloP100		-1.2

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: rs7023003;

hg19: chr9-107880670;