6-25069135-A-G

Variant names:

• chr6-25069135-A-G
• rs302966
• ENST00000648291.1:n.206A>G

Variant summary

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

The ENST00000648291.1(ENSG00000285801):​n.206A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.835 in 152,128 control chromosomes in the GnomAD database, including 53,151 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 0.84 (53151 hom., cov: 31)
• Consequence: ENSG00000285801 ENST00000648291.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.392
• Publications: 3 publications found

Genes affected

ENSG00000285801 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.852 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000648291.1. 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
	ENSG00000285801	ENST00000648291.1		n.206A>G		non_coding_transcript_exon	Exon 2 of 6
	CMAHP	ENST00000424868.2	TSL:3	n.678-3209T>C		intron	N/A
	ENSG00000288887	ENST00000761912.1		n.735-9478A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.835 AC: 126962 AN: 152010 Hom.: 53101 Cov.: 31

Gnomad AFR AF: 0.807

Gnomad AMI AF: 0.893

Gnomad AMR AF: 0.863

Gnomad ASJ AF: 0.871

Gnomad EAS AF: 0.865

Gnomad SAS AF: 0.873

Gnomad FIN AF: 0.846

Gnomad MID AF: 0.899

Gnomad NFE AF: 0.836

Gnomad OTH AF: 0.842

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

GnomAD4 genome AF: 0.835 AC: 127067 AN: 152128 Hom.: 53151 Cov.: 31 AF XY: 0.837 AC XY: 62238 AN XY: 74382

African (AFR) AF: 0.807 AC: 33476 AN: 41480

American (AMR) AF: 0.863 AC: 13188 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.871 AC: 3023 AN: 3472

East Asian (EAS) AF: 0.865 AC: 4469 AN: 5168

South Asian (SAS) AF: 0.874 AC: 4207 AN: 4814

European-Finnish (FIN) AF: 0.846 AC: 8961 AN: 10588

Middle Eastern (MID) AF: 0.905 AC: 266 AN: 294

European-Non Finnish (NFE) AF: 0.836 AC: 56888 AN: 68020

Other (OTH) AF: 0.844 AC: 1775 AN: 2104

Alfa AF: 0.833 Hom.: 6813

Bravo AF: 0.834

Asia WGS AF: 0.890 AC: 3095 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.5
DANN	Benign	0.73
PhyloP100		-0.39

Splicing

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

Other links and lift over

dbSNP: rs302966; hg19: chr6-25069363;