2-217449530-C-T

Position:

• chr2-217449530-C-T

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_Strong BS2

The NR_026597.2(DIRC3):​n.1523-15414G>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 0.00605 in 120,802 control chromosomes in the GnomAD database, including 6 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 0.0061 (6 hom., cov: 30)
• Consequence: DIRC3 NR_026597.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.17

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.1).
• BS2: High Homozygotes in GnomAd4 at 6 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DIRC3	NR_026597.2	n.1523-15414G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DIRC3	ENST00000486365.5	n.1523-15414G>A		intron_variant, non_coding_transcript_variant		5
DIRC3	ENST00000474063.5	n.500-15414G>A		intron_variant, non_coding_transcript_variant		2
DIRC3	ENST00000663562.1	n.1610-15414G>A		intron_variant, non_coding_transcript_variant
DIRC3	ENST00000676082.1	n.273-15414G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.00604 AC: 729 AN: 120660 Hom.: 6 Cov.: 30

Gnomad AFR AF: 0.0144

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00501

Gnomad ASJ AF: 0.00895

Gnomad EAS AF: 0.0157

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000877

Gnomad OTH AF: 0.00478

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

GnomAD4 genome AF: 0.00605 AC: 731 AN: 120802 Hom.: 6 Cov.: 30 AF XY: 0.00610 AC XY: 363 AN XY: 59500

Gnomad4 AFR AF: 0.0144

Gnomad4 AMR AF: 0.00500

Gnomad4 ASJ AF: 0.00895

Gnomad4 EAS AF: 0.0158

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000878

Gnomad4 OTH AF: 0.00471

Alfa AF: 0.114 Hom.: 168

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.059
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11689435; hg19: chr2-218314253;