rs2393667

Variant names:

• chr6-26421117-T-C
• rs2393667
• ENST00000707189.1:n.1000-132070T>C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000707189.1(ENSG00000291336):​n.1000-132070T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0767 in 152,060 control chromosomes in the GnomAD database, including 558 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 0.077 (558 hom., cov: 31)
• Consequence: ENSG00000291336 ENST00000707189.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.189

Genes affected

ENSG00000291336 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.108 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000291336	ENST00000707189.1	n.1000-132070T>C		intron_variant	Intron 1 of 1
ENSG00000291338	ENST00000707191.1	n.1001-111588T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0768 AC: 11671 AN: 151942 Hom.: 559 Cov.: 31

Gnomad AFR AF: 0.0334

Gnomad AMI AF: 0.196

Gnomad AMR AF: 0.0384

Gnomad ASJ AF: 0.0375

Gnomad EAS AF: 0.0992

Gnomad SAS AF: 0.0998

Gnomad FIN AF: 0.0764

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.110

Gnomad OTH AF: 0.0627

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

GnomAD4 genome AF: 0.0767 AC: 11664 AN: 152060 Hom.: 558 Cov.: 31 AF XY: 0.0739 AC XY: 5495 AN XY: 74318

Gnomad4 AFR AF: 0.0334

Gnomad4 AMR AF: 0.0382

Gnomad4 ASJ AF: 0.0375

Gnomad4 EAS AF: 0.0995

Gnomad4 SAS AF: 0.0989

Gnomad4 FIN AF: 0.0764

Gnomad4 NFE AF: 0.110

Gnomad4 OTH AF: 0.0630

Alfa AF: 0.101 Hom.: 256

Bravo AF: 0.0713

Asia WGS AF: 0.104 AC: 362 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	6.3
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2393667; hg19: chr6-26421345;