20-1425568-T-C

Variant names:

• chr20-1425568-T-C
• rs6042209
• ENST00000740734.1:n.125-6564A>G

Variant summary

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

The ENST00000740734.1(ENSG00000296607):​n.125-6564A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.811 in 151,970 control chromosomes in the GnomAD database, including 49,974 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 0.81 (49974 hom., cov: 30)
• Consequence: ENSG00000296607 ENST00000740734.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.69
• Publications: 10 publications found

Genes affected

ENSG00000296607 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.849 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000740734.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000296607	ENST00000740734.1		n.125-6564A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.811 AC: 123136 AN: 151850 Hom.: 49932 Cov.: 30

Gnomad AFR AF: 0.857

Gnomad AMI AF: 0.865

Gnomad AMR AF: 0.785

Gnomad ASJ AF: 0.739

Gnomad EAS AF: 0.811

Gnomad SAS AF: 0.768

Gnomad FIN AF: 0.734

Gnomad MID AF: 0.771

Gnomad NFE AF: 0.808

Gnomad OTH AF: 0.793

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

GnomAD4 genome AF: 0.811 AC: 123242 AN: 151970 Hom.: 49974 Cov.: 30 AF XY: 0.806 AC XY: 59840 AN XY: 74260

African (AFR) AF: 0.857 AC: 35479 AN: 41418

American (AMR) AF: 0.785 AC: 11980 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.739 AC: 2564 AN: 3470

East Asian (EAS) AF: 0.810 AC: 4188 AN: 5168

South Asian (SAS) AF: 0.768 AC: 3702 AN: 4820

European-Finnish (FIN) AF: 0.734 AC: 7739 AN: 10546

Middle Eastern (MID) AF: 0.779 AC: 229 AN: 294

European-Non Finnish (NFE) AF: 0.808 AC: 54891 AN: 67968

Other (OTH) AF: 0.795 AC: 1681 AN: 2114

Alfa AF: 0.807 Hom.: 158116

Bravo AF: 0.820

Asia WGS AF: 0.789 AC: 2743 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.24
DANN	Benign	0.52
PhyloP100		-1.7

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs6042209;

hg19: chr20-1406212;