rs9283880

Variant names:

• chr6-27747464-A-C
• rs9283880
• ENST00000783576.1:n.245-4325T>G

Your query was ambiguous. Multiple possible variants found:

• chr6-27747464-A-C
• chr6-27747464-A-T

Variant summary

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

The ENST00000783576.1(ENSG00000302043):​n.245-4325T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.33 in 152,028 control chromosomes in the GnomAD database, including 9,983 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 0.33 (9983 hom., cov: 32)
• Consequence: ENSG00000302043 ENST00000783576.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.04
• Publications: 18 publications found

Genes affected

ENSG00000302043 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.555 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000783576.1. 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
	ENSG00000302043	ENST00000783576.1		n.245-4325T>G		intron	N/A
	ENSG00000302043	ENST00000783577.1		n.203+6595T>G		intron	N/A
	ENSG00000302043	ENST00000783578.1		n.191-4325T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.330 AC: 50114 AN: 151910 Hom.: 9957 Cov.: 32

Gnomad AFR AF: 0.561

Gnomad AMI AF: 0.389

Gnomad AMR AF: 0.292

Gnomad ASJ AF: 0.164

Gnomad EAS AF: 0.195

Gnomad SAS AF: 0.247

Gnomad FIN AF: 0.191

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.245

Gnomad OTH AF: 0.314

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

GnomAD4 genome AF: 0.330 AC: 50184 AN: 152028 Hom.: 9983 Cov.: 32 AF XY: 0.324 AC XY: 24105 AN XY: 74322

African (AFR) AF: 0.561 AC: 23235 AN: 41412

American (AMR) AF: 0.292 AC: 4464 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.164 AC: 570 AN: 3470

East Asian (EAS) AF: 0.195 AC: 1009 AN: 5182

South Asian (SAS) AF: 0.247 AC: 1194 AN: 4828

European-Finnish (FIN) AF: 0.191 AC: 2014 AN: 10568

Middle Eastern (MID) AF: 0.218 AC: 64 AN: 294

European-Non Finnish (NFE) AF: 0.245 AC: 16623 AN: 67964

Other (OTH) AF: 0.311 AC: 656 AN: 2110

Alfa AF: 0.282 Hom.: 14916

Bravo AF: 0.349

Asia WGS AF: 0.245 AC: 853 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	2.5
DANN	Benign	0.43
PhyloP100		-1.0

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: rs9283880;

hg19: chr6-27715243;

COSMIC: COSV69399382;