chr2-217043749-A-G

Variant names:

• chr2-217043749-A-G
• rs10490444
• ENST00000695932.1:n.509+49731A>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+49731A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.401 in 152,062 control chromosomes in the GnomAD database, including 12,718 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 0.40 (12718 hom., cov: 32)
• Consequence: DIRC3-AS1 ENST00000695932.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.229

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 = 0.465 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+49731A>G		intron_variant	Intron 3 of 11
DIRC3-AS1	ENST00000695934.1	n.172+49731A>G		intron_variant	Intron 3 of 8
DIRC3-AS1	ENST00000695937.1	n.289+6469A>G		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.401 AC: 60993 AN: 151944 Hom.: 12705 Cov.: 32

Gnomad AFR AF: 0.471

Gnomad AMI AF: 0.439

Gnomad AMR AF: 0.332

Gnomad ASJ AF: 0.461

Gnomad EAS AF: 0.102

Gnomad SAS AF: 0.378

Gnomad FIN AF: 0.294

Gnomad MID AF: 0.487

Gnomad NFE AF: 0.412

Gnomad OTH AF: 0.401

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

GnomAD4 genome AF: 0.401 AC: 61048 AN: 152062 Hom.: 12718 Cov.: 32 AF XY: 0.392 AC XY: 29132 AN XY: 74328

Gnomad4 AFR AF: 0.471

Gnomad4 AMR AF: 0.332

Gnomad4 ASJ AF: 0.461

Gnomad4 EAS AF: 0.102

Gnomad4 SAS AF: 0.379

Gnomad4 FIN AF: 0.294

Gnomad4 NFE AF: 0.412

Gnomad4 OTH AF: 0.404

Alfa AF: 0.379 Hom.: 6200

Bravo AF: 0.406

Asia WGS AF: 0.248 AC: 862 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.49
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10490444; hg19: chr2-217908472;