rs9283878

Variant names:

• chr6-26754842-G-A
• rs9283878
• ENST00000794331.1:n.101C>T

Your query was ambiguous. Multiple possible variants found:

• chr6-26754842-G-A
• chr6-26754842-G-C
• chr6-26754842-G-T

Variant summary

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

The ENST00000794331.1(ENSG00000303414):​n.101C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0303 in 128,002 control chromosomes in the GnomAD database, including 289 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 0.030 (289 hom., cov: 22)
• Consequence: ENSG00000303414 ENST00000794331.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.998
• Publications: 1 publications found

Genes affected

ENSG00000303414 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0778 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000794331.1. 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
	ENSG00000303414	ENST00000794331.1		n.101C>T		non_coding_transcript_exon	Exon 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0302 AC: 3868 AN: 127908 Hom.: 288 Cov.: 22

Gnomad AFR AF: 0.0801

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0222

Gnomad ASJ AF: 0.0224

Gnomad EAS AF: 0.0205

Gnomad SAS AF: 0.00261

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.0224

Gnomad NFE AF: 0.00354

Gnomad OTH AF: 0.0325

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

GnomAD4 genome AF: 0.0303 AC: 3878 AN: 128002 Hom.: 289 Cov.: 22 AF XY: 0.0297 AC XY: 1847 AN XY: 62086

African (AFR) AF: 0.0801 AC: 3219 AN: 40206

American (AMR) AF: 0.0222 AC: 274 AN: 12330

Ashkenazi Jewish (ASJ) AF: 0.0224 AC: 59 AN: 2636

East Asian (EAS) AF: 0.0205 AC: 60 AN: 2926

South Asian (SAS) AF: 0.00261 AC: 8 AN: 3070

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 8898

Middle Eastern (MID) AF: 0.0242 AC: 6 AN: 248

European-Non Finnish (NFE) AF: 0.00354 AC: 195 AN: 55124

Other (OTH) AF: 0.0324 AC: 57 AN: 1758

Alfa AF: 0.0182 Hom.: 20

Asia WGS AF: 0.0140 AC: 34 AN: 2338

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	11
DANN	Uncertain	0.98
PhyloP100		1.0

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs9283878; hg19: chr6-26747038;