2-217051329-T-G

Variant names:

• chr2-217051329-T-G
• rs12613955
• ENST00000695932.1:n.509+57311T>G

Variant summary

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

The ENST00000695932.1(DIRC3-AS1):​n.509+57311T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.503 in 151,996 control chromosomes in the GnomAD database, including 19,889 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 0.50 (19889 hom., cov: 32)
• Consequence: DIRC3-AS1 ENST00000695932.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.21

Genes affected

DIRC3-AS1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.875 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	ENST00000695932.1	n.509+57311T>G		intron_variant	Intron 3 of 11
DIRC3-AS1	ENST00000695934.1	n.172+57311T>G		intron_variant	Intron 3 of 8
DIRC3-AS1	ENST00000695937.1	n.290-3862T>G		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.503 AC: 76396 AN: 151878 Hom.: 19858 Cov.: 32

Gnomad AFR AF: 0.512

Gnomad AMI AF: 0.374

Gnomad AMR AF: 0.590

Gnomad ASJ AF: 0.433

Gnomad EAS AF: 0.896

Gnomad SAS AF: 0.492

Gnomad FIN AF: 0.469

Gnomad MID AF: 0.399

Gnomad NFE AF: 0.460

Gnomad OTH AF: 0.506

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

GnomAD4 genome AF: 0.503 AC: 76479 AN: 151996 Hom.: 19889 Cov.: 32 AF XY: 0.505 AC XY: 37523 AN XY: 74304

Gnomad4 AFR AF: 0.512

Gnomad4 AMR AF: 0.590

Gnomad4 ASJ AF: 0.433

Gnomad4 EAS AF: 0.896

Gnomad4 SAS AF: 0.493

Gnomad4 FIN AF: 0.469

Gnomad4 NFE AF: 0.460

Gnomad4 OTH AF: 0.513

Alfa AF: 0.465 Hom.: 5528

Bravo AF: 0.516

Asia WGS AF: 0.736 AC: 2558 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	11
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12613955; hg19: chr2-217916052;