rs2553026

Variant names:

• chr2-217258925-G-A
• rs2553026
• ENST00000695932.1:n.510-2735G>A

Your query was ambiguous. Multiple possible variants found:

• chr2-217258925-G-A
• chr2-217258925-G-C
• chr2-217258925-G-T

Variant summary

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

The ENST00000695932.1(DIRC3-AS1):​n.510-2735G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.525 in 151,988 control chromosomes in the GnomAD database, including 25,191 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 0.53 (25191 hom., cov: 31)
• Consequence: DIRC3-AS1 ENST00000695932.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.252

Genes affected

DIRC3-AS1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.716 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.510-2735G>A		intron_variant	Intron 3 of 11
DIRC3-AS1	ENST00000695934.1	n.714-379G>A		intron_variant	Intron 5 of 8
DIRC3-AS1	ENST00000695940.1	n.581-379G>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.526 AC: 79821 AN: 151872 Hom.: 25188 Cov.: 31

Gnomad AFR AF: 0.178

Gnomad AMI AF: 0.582

Gnomad AMR AF: 0.599

Gnomad ASJ AF: 0.530

Gnomad EAS AF: 0.263

Gnomad SAS AF: 0.544

Gnomad FIN AF: 0.633

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.721

Gnomad OTH AF: 0.540

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

GnomAD4 genome AF: 0.525 AC: 79835 AN: 151988 Hom.: 25191 Cov.: 31 AF XY: 0.520 AC XY: 38619 AN XY: 74290

Gnomad4 AFR AF: 0.178

Gnomad4 AMR AF: 0.598

Gnomad4 ASJ AF: 0.530

Gnomad4 EAS AF: 0.262

Gnomad4 SAS AF: 0.545

Gnomad4 FIN AF: 0.633

Gnomad4 NFE AF: 0.721

Gnomad4 OTH AF: 0.543

Alfa AF: 0.670 Hom.: 35288

Bravo AF: 0.508

Asia WGS AF: 0.388 AC: 1351 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	8.8
DANN	Benign	0.85

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2553026; hg19: chr2-218123648;