rs13013872

Variant names:

• chr2-217091812-A-G
• rs13013872
• ENST00000695932.1:n.509+97794A>G

Your query was ambiguous. Multiple possible variants found:

• chr2-217091812-A-G
• chr2-217091812-A-T

Variant summary

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

The ENST00000695932.1(DIRC3-AS1):​n.509+97794A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.614 in 148,878 control chromosomes in the GnomAD database, including 30,594 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 0.61 (30594 hom., cov: 31)
• Consequence: DIRC3-AS1 ENST00000695932.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.124

Genes affected

DIRC3-AS1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.787 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+97794A>G		intron_variant	Intron 3 of 11
DIRC3-AS1	ENST00000695934.1	n.173-61599A>G		intron_variant	Intron 3 of 8

Frequencies

GnomAD3 genomes AF: 0.614 AC: 91287 AN: 148762 Hom.: 30551 Cov.: 31

Gnomad AFR AF: 0.794

Gnomad AMI AF: 0.456

Gnomad AMR AF: 0.649

Gnomad ASJ AF: 0.530

Gnomad EAS AF: 0.412

Gnomad SAS AF: 0.576

Gnomad FIN AF: 0.446

Gnomad MID AF: 0.637

Gnomad NFE AF: 0.552

Gnomad OTH AF: 0.607

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

GnomAD4 genome AF: 0.614 AC: 91389 AN: 148878 Hom.: 30594 Cov.: 31 AF XY: 0.608 AC XY: 44222 AN XY: 72760

Gnomad4 AFR AF: 0.794

Gnomad4 AMR AF: 0.649

Gnomad4 ASJ AF: 0.530

Gnomad4 EAS AF: 0.411

Gnomad4 SAS AF: 0.577

Gnomad4 FIN AF: 0.446

Gnomad4 NFE AF: 0.552

Gnomad4 OTH AF: 0.605

Alfa AF: 0.590 Hom.: 4732

Bravo AF: 0.639

Asia WGS AF: 0.517 AC: 1798 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.5
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13013872; hg19: chr2-217956535;