2-217445617-C-T

Position:

• chr2-217445617-C-T

Variant summary

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

The NR_026597.2(DIRC3):​n.1523-11501G>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 0.439 in 152,038 control chromosomes in the GnomAD database, including 16,843 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 0.44 (16843 hom., cov: 32)
• Consequence: DIRC3 NR_026597.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.61

Genes affected

DIRC3 (HGNC:17805): (disrupted in renal carcinoma 3)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.583 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DIRC3	NR_026597.2	n.1523-11501G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DIRC3	ENST00000486365.5	n.1523-11501G>A		intron_variant, non_coding_transcript_variant		5
DIRC3	ENST00000474063.5	n.500-11501G>A		intron_variant, non_coding_transcript_variant		2
DIRC3	ENST00000663562.1	n.1610-11501G>A		intron_variant, non_coding_transcript_variant
DIRC3	ENST00000676082.1	n.273-11501G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.440 AC: 66789 AN: 151920 Hom.: 16848 Cov.: 32

Gnomad AFR AF: 0.216

Gnomad AMI AF: 0.468

Gnomad AMR AF: 0.419

Gnomad ASJ AF: 0.617

Gnomad EAS AF: 0.220

Gnomad SAS AF: 0.246

Gnomad FIN AF: 0.513

Gnomad MID AF: 0.576

Gnomad NFE AF: 0.588

Gnomad OTH AF: 0.484

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

GnomAD4 genome AF: 0.439 AC: 66787 AN: 152038 Hom.: 16843 Cov.: 32 AF XY: 0.434 AC XY: 32267 AN XY: 74322

Gnomad4 AFR AF: 0.215

Gnomad4 AMR AF: 0.418

Gnomad4 ASJ AF: 0.617

Gnomad4 EAS AF: 0.220

Gnomad4 SAS AF: 0.248

Gnomad4 FIN AF: 0.513

Gnomad4 NFE AF: 0.588

Gnomad4 OTH AF: 0.478

Alfa AF: 0.557 Hom.: 52888

Bravo AF: 0.424

Asia WGS AF: 0.204 AC: 710 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	8.5
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs966423; hg19: chr2-218310340;