rs1011502

Variant names:

• chr2-216943480-T-G
• rs1011502
• ENST00000447289.1:n.511-50478T>G

Variant summary

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

The ENST00000607591.1(DIRC3-AS1):​n.114-38491T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.332 in 152,182 control chromosomes in the GnomAD database, including 8,793 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 0.33 (8793 hom., cov: 33)
• Consequence: DIRC3-AS1 ENST00000607591.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.511

Genes affected

DIRC3-AS1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.412 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.511-50478T>G		intron_variant	Intron 3 of 3	5
DIRC3-AS1	ENST00000607591.1	n.114-38491T>G		intron_variant	Intron 1 of 2	3
DIRC3-AS1	ENST00000695932.1	n.449-50478T>G		intron_variant	Intron 2 of 11

Frequencies

GnomAD3 genomes AF: 0.333 AC: 50565 AN: 152064 Hom.: 8785 Cov.: 33

Gnomad AFR AF: 0.246

Gnomad AMI AF: 0.228

Gnomad AMR AF: 0.376

Gnomad ASJ AF: 0.307

Gnomad EAS AF: 0.265

Gnomad SAS AF: 0.427

Gnomad FIN AF: 0.360

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.372

Gnomad OTH AF: 0.337

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

GnomAD4 genome AF: 0.332 AC: 50595 AN: 152182 Hom.: 8793 Cov.: 33 AF XY: 0.334 AC XY: 24879 AN XY: 74398

Gnomad4 AFR AF: 0.246

Gnomad4 AMR AF: 0.376

Gnomad4 ASJ AF: 0.307

Gnomad4 EAS AF: 0.265

Gnomad4 SAS AF: 0.428

Gnomad4 FIN AF: 0.360

Gnomad4 NFE AF: 0.372

Gnomad4 OTH AF: 0.337

Alfa AF: 0.360 Hom.: 6641

Bravo AF: 0.328

Asia WGS AF: 0.354 AC: 1230 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	7.3
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: rs1011502; hg19: chr2-217808203;