rs2393667

Positions:

• chr6-26421117-T-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, non coding transcript 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: ENST00000707189.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.189

Genes affected

(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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000707189.1	n.1000-132070T>C		intron_variant, non_coding_transcript_variant
	ENST00000707191.1	n.1001-111588T>C		intron_variant, non_coding_transcript_variant

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;