rs2553026

chr2-217258925-G-Achr2-217258925-G-Cchr2-217258925-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, non coding transcript 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, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.252

Genes affected

DIRC3-AS1 (HGNC:50636): (DIRC3 antisense RNA 1)

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DIRC3-AS1	ENST00000695932.1	n.510-2735G>A		intron_variant, non_coding_transcript_variant
DIRC3-AS1	ENST00000695934.1	n.714-379G>A		intron_variant, non_coding_transcript_variant
DIRC3-AS1	ENST00000695940.1	n.581-379G>A		intron_variant, non_coding_transcript_variant

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;