6-126499415-T-G

Variant names:

• chr6-126499415-T-G
• rs2130604
• ENST00000650727.1:n.3037-1890A>C

Variant summary

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

The ENST00000650727.1(ENSG00000286215):​n.3037-1890A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.759 in 151,878 control chromosomes in the GnomAD database, including 44,225 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 0.76 (44225 hom., cov: 31)
• Consequence: ENSG00000286215 ENST00000650727.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.755

Genes affected

ENSG00000286215 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.974 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.3037-1890A>C		intron_variant	Intron 14 of 14
ENSG00000286215	ENST00000651326.1	n.2290-26821A>C		intron_variant	Intron 5 of 6
ENSG00000286215	ENST00000652383.1	n.630+32248A>C		intron_variant	Intron 3 of 4
ENSG00000286215	ENST00000652545.1	n.3347-1890A>C		intron_variant	Intron 15 of 15

Frequencies

GnomAD3 genomes AF: 0.759 AC: 115115 AN: 151760 Hom.: 44173 Cov.: 31

Gnomad AFR AF: 0.684

Gnomad AMI AF: 0.764

Gnomad AMR AF: 0.838

Gnomad ASJ AF: 0.754

Gnomad EAS AF: 0.997

Gnomad SAS AF: 0.951

Gnomad FIN AF: 0.681

Gnomad MID AF: 0.832

Gnomad NFE AF: 0.766

Gnomad OTH AF: 0.769

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

GnomAD4 genome AF: 0.759 AC: 115230 AN: 151878 Hom.: 44225 Cov.: 31 AF XY: 0.761 AC XY: 56461 AN XY: 74236

Gnomad4 AFR AF: 0.684

Gnomad4 AMR AF: 0.839

Gnomad4 ASJ AF: 0.754

Gnomad4 EAS AF: 0.997

Gnomad4 SAS AF: 0.951

Gnomad4 FIN AF: 0.681

Gnomad4 NFE AF: 0.766

Gnomad4 OTH AF: 0.772

Alfa AF: 0.757 Hom.: 5431

Bravo AF: 0.765

Asia WGS AF: 0.939 AC: 3260 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.79
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2130604; hg19: chr6-126820561;