chr2-216991469-G-A

Variant names:

• chr2-216991469-G-A
• rs2542197
• ENST00000447289.1:n.511-2489G>A

Variant summary

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

The ENST00000607591.1(DIRC3-AS1):​n.273-2489G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.484 in 152,118 control chromosomes in the GnomAD database, including 19,250 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 0.48 (19250 hom., cov: 33)
• Consequence: DIRC3-AS1 ENST00000607591.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.38

Genes affected

DIRC3-AS1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.732 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.511-2489G>A		intron_variant	Intron 3 of 3	5
DIRC3-AS1	ENST00000607591.1	n.273-2489G>A		intron_variant	Intron 2 of 2	3
DIRC3-AS1	ENST00000695932.1	n.449-2489G>A		intron_variant	Intron 2 of 11

Frequencies

GnomAD3 genomes AF: 0.484 AC: 73555 AN: 152000 Hom.: 19213 Cov.: 33

Gnomad AFR AF: 0.671

Gnomad AMI AF: 0.253

Gnomad AMR AF: 0.501

Gnomad ASJ AF: 0.376

Gnomad EAS AF: 0.752

Gnomad SAS AF: 0.525

Gnomad FIN AF: 0.297

Gnomad MID AF: 0.380

Gnomad NFE AF: 0.381

Gnomad OTH AF: 0.474

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

GnomAD4 genome AF: 0.484 AC: 73642 AN: 152118 Hom.: 19250 Cov.: 33 AF XY: 0.484 AC XY: 35992 AN XY: 74354

Gnomad4 AFR AF: 0.671

Gnomad4 AMR AF: 0.502

Gnomad4 ASJ AF: 0.376

Gnomad4 EAS AF: 0.752

Gnomad4 SAS AF: 0.523

Gnomad4 FIN AF: 0.297

Gnomad4 NFE AF: 0.381

Gnomad4 OTH AF: 0.471

Alfa AF: 0.406 Hom.: 14049

Bravo AF: 0.508

Asia WGS AF: 0.632 AC: 2198 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.85
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2542197; hg19: chr2-217856192;