rs2244235

Variant names:

• chr2-216968676-C-T
• rs2244235
• ENST00000447289.1:n.511-25282C>T

Variant summary

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

The ENST00000607591.1(DIRC3-AS1):​n.114-13295C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.667 in 152,068 control chromosomes in the GnomAD database, including 34,900 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 0.67 (34900 hom., cov: 31)
• Consequence: DIRC3-AS1 ENST00000607591.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.171

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 (AFR) allele frequency at 95% confidence interval = 0.834 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.511-25282C>T		intron_variant	Intron 3 of 3	5
DIRC3-AS1	ENST00000607591.1	n.114-13295C>T		intron_variant	Intron 1 of 2	3
DIRC3-AS1	ENST00000695932.1	n.449-25282C>T		intron_variant	Intron 2 of 11

Frequencies

GnomAD3 genomes AF: 0.667 AC: 101324 AN: 151950 Hom.: 34853 Cov.: 31

Gnomad AFR AF: 0.841

Gnomad AMI AF: 0.635

Gnomad AMR AF: 0.619

Gnomad ASJ AF: 0.653

Gnomad EAS AF: 0.756

Gnomad SAS AF: 0.553

Gnomad FIN AF: 0.581

Gnomad MID AF: 0.630

Gnomad NFE AF: 0.588

Gnomad OTH AF: 0.663

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

GnomAD4 genome AF: 0.667 AC: 101425 AN: 152068 Hom.: 34900 Cov.: 31 AF XY: 0.663 AC XY: 49241 AN XY: 74302

Gnomad4 AFR AF: 0.841

Gnomad4 AMR AF: 0.619

Gnomad4 ASJ AF: 0.653

Gnomad4 EAS AF: 0.756

Gnomad4 SAS AF: 0.553

Gnomad4 FIN AF: 0.581

Gnomad4 NFE AF: 0.588

Gnomad4 OTH AF: 0.663

Alfa AF: 0.638 Hom.: 4082

Bravo AF: 0.679

Asia WGS AF: 0.658 AC: 2288 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.1
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2244235; hg19: chr2-217833399;