ENST00000447289.1:n.511-7172G>T

Variant names:

• chr2-216986786-G-T
• rs1882420
• ENST00000447289.1:n.511-7172G>T

Variant summary

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

The ENST00000447289.1(DIRC3-AS1):​n.511-7172G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.299 in 152,046 control chromosomes in the GnomAD database, including 11,291 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 0.30 (11291 hom., cov: 32)
• Consequence: DIRC3-AS1 ENST00000447289.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.24

Genes affected

DIRC3-AS1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.673 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
DIRC3-AS1	ENST00000447289.1	n.511-7172G>T		intron_variant	Intron 3 of 3	5
DIRC3-AS1	ENST00000607591.1	n.272+4657G>T		intron_variant	Intron 2 of 2	3
DIRC3-AS1	ENST00000695932.1	n.449-7172G>T		intron_variant	Intron 2 of 11

Frequencies

GnomAD3 genomes AF: 0.299 AC: 45352 AN: 151928 Hom.: 11249 Cov.: 32

Gnomad AFR AF: 0.679

Gnomad AMI AF: 0.248

Gnomad AMR AF: 0.263

Gnomad ASJ AF: 0.113

Gnomad EAS AF: 0.148

Gnomad SAS AF: 0.143

Gnomad FIN AF: 0.210

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.124

Gnomad OTH AF: 0.258

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

GnomAD4 genome AF: 0.299 AC: 45453 AN: 152046 Hom.: 11291 Cov.: 32 AF XY: 0.300 AC XY: 22262 AN XY: 74312

Gnomad4 AFR AF: 0.680

Gnomad4 AMR AF: 0.263

Gnomad4 ASJ AF: 0.113

Gnomad4 EAS AF: 0.148

Gnomad4 SAS AF: 0.142

Gnomad4 FIN AF: 0.210

Gnomad4 NFE AF: 0.124

Gnomad4 OTH AF: 0.254

Alfa AF: 0.147 Hom.: 3440

Bravo AF: 0.322

Asia WGS AF: 0.181 AC: 628 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.13
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1882420; hg19: chr2-217851509;