6-126794309-C-T

Variant names:

• chr6-126794309-C-T
• rs13209747
• ENST00000650727.1:n.1166+25083G>A

Variant summary

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

The ENST00000650727.1(ENSG00000286215):​n.1166+25083G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.365 in 151,948 control chromosomes in the GnomAD database, including 11,414 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 0.36 (11414 hom., cov: 32)
• Consequence: ENSG00000286215 ENST00000650727.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.60

Genes affected

ENSG00000286215 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.459 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
ENSG00000286215	ENST00000650727.1	n.1166+25083G>A		intron_variant	Intron 9 of 14
ENSG00000286215	ENST00000650823.1	n.1251+25083G>A		intron_variant	Intron 10 of 11
ENSG00000286215	ENST00000650876.1	n.831-33302G>A		intron_variant	Intron 6 of 7

Frequencies

GnomAD3 genomes AF: 0.365 AC: 55437 AN: 151830 Hom.: 11417 Cov.: 32

Gnomad AFR AF: 0.160

Gnomad AMI AF: 0.545

Gnomad AMR AF: 0.370

Gnomad ASJ AF: 0.450

Gnomad EAS AF: 0.475

Gnomad SAS AF: 0.434

Gnomad FIN AF: 0.519

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.445

Gnomad OTH AF: 0.367

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

GnomAD4 genome AF: 0.365 AC: 55420 AN: 151948 Hom.: 11414 Cov.: 32 AF XY: 0.371 AC XY: 27524 AN XY: 74278

Gnomad4 AFR AF: 0.159

Gnomad4 AMR AF: 0.370

Gnomad4 ASJ AF: 0.450

Gnomad4 EAS AF: 0.475

Gnomad4 SAS AF: 0.435

Gnomad4 FIN AF: 0.519

Gnomad4 NFE AF: 0.445

Gnomad4 OTH AF: 0.362

Alfa AF: 0.417 Hom.: 6914

Bravo AF: 0.343

Asia WGS AF: 0.403 AC: 1400 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.35
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13209747; hg19: chr6-127115454;