ENST00000716595.1:n.51-1972T>G

Variant names:

• chr9-34071543-T-G
• rs7871764
• ENST00000716595.1:n.51-1972T>G

Variant summary

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

The ENST00000716595.1(DCAF12-AS1):​n.51-1972T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.646 in 151,746 control chromosomes in the GnomAD database, including 32,797 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 0.65 (32797 hom., cov: 30)
• Consequence: DCAF12-AS1 ENST00000716595.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.780
• Publications: 20 publications found

Genes affected

DCAF12-AS1 (HGNC:58097):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.879 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000716595.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DCAF12-AS1	ENST00000716595.1		n.51-1972T>G		intron	N/A
	DCAF12-AS1	ENST00000716596.1		n.49-1972T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.647 AC: 98060 AN: 151626 Hom.: 32795 Cov.: 30

Gnomad AFR AF: 0.474

Gnomad AMI AF: 0.568

Gnomad AMR AF: 0.691

Gnomad ASJ AF: 0.721

Gnomad EAS AF: 0.901

Gnomad SAS AF: 0.809

Gnomad FIN AF: 0.637

Gnomad MID AF: 0.744

Gnomad NFE AF: 0.707

Gnomad OTH AF: 0.696

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

GnomAD4 genome AF: 0.646 AC: 98101 AN: 151746 Hom.: 32797 Cov.: 30 AF XY: 0.649 AC XY: 48121 AN XY: 74148

African (AFR) AF: 0.474 AC: 19580 AN: 41330

American (AMR) AF: 0.691 AC: 10512 AN: 15212

Ashkenazi Jewish (ASJ) AF: 0.721 AC: 2501 AN: 3470

East Asian (EAS) AF: 0.901 AC: 4652 AN: 5164

South Asian (SAS) AF: 0.808 AC: 3898 AN: 4822

European-Finnish (FIN) AF: 0.637 AC: 6700 AN: 10510

Middle Eastern (MID) AF: 0.743 AC: 217 AN: 292

European-Non Finnish (NFE) AF: 0.707 AC: 48053 AN: 67930

Other (OTH) AF: 0.698 AC: 1471 AN: 2106

Alfa AF: 0.698 Hom.: 171272

Bravo AF: 0.646

Asia WGS AF: 0.808 AC: 2808 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	2.1
DANN	Benign	0.80
PhyloP100		-0.78

Splicing

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

Other links and lift over

dbSNP: rs7871764; hg19: chr9-34071541; COSMIC: COSV60352980;