chr6-126499415-T-G

Variant names:

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

Variant summary

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

The ENST00000650727.1(ENSG00000293110):​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: ENSG00000293110 ENST00000650727.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.755
• Publications: 15 publications found

Genes affected

ENSG00000293110 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000650727.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000293110	ENST00000650727.1		n.3037-1890A>C		intron	N/A
	ENSG00000293110	ENST00000651326.1		n.2290-26821A>C		intron	N/A
	ENSG00000293110	ENST00000652383.1		n.630+32248A>C		intron	N/A

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

African (AFR) AF: 0.684 AC: 28351 AN: 41424

American (AMR) AF: 0.839 AC: 12802 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.754 AC: 2618 AN: 3470

East Asian (EAS) AF: 0.997 AC: 5157 AN: 5172

South Asian (SAS) AF: 0.951 AC: 4581 AN: 4816

European-Finnish (FIN) AF: 0.681 AC: 7185 AN: 10546

Middle Eastern (MID) AF: 0.837 AC: 246 AN: 294

European-Non Finnish (NFE) AF: 0.766 AC: 51962 AN: 67866

Other (OTH) AF: 0.772 AC: 1631 AN: 2112

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.79
DANN	Benign	0.50
PhyloP100		-0.76

Splicing

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

Other links and lift over

dbSNP: rs2130604; hg19: chr6-126820561;