rs11695415

Positions:

• chr2-217273761-T-C
• chr2-217273761-T-G

Variant summary

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

The ENST00000695932.1(DIRC3-AS1):​n.854-3837T>C 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 0.186 in 151,888 control chromosomes in the GnomAD database, including 2,709 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 0.19 (2709 hom., cov: 31)
• Consequence: DIRC3-AS1 ENST00000695932.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.132

Genes affected

DIRC3-AS1 (HGNC:50636): (DIRC3 antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.285 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DIRC3-AS1	ENST00000695932.1	n.854-3837T>C		intron_variant, non_coding_transcript_variant
DIRC3-AS1	ENST00000655995.1	n.420-3837T>C		intron_variant, non_coding_transcript_variant
DIRC3-AS1	ENST00000657920.1	n.420-3837T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.186 AC: 28186 AN: 151770 Hom.: 2708 Cov.: 31

Gnomad AFR AF: 0.212

Gnomad AMI AF: 0.264

Gnomad AMR AF: 0.193

Gnomad ASJ AF: 0.143

Gnomad EAS AF: 0.297

Gnomad SAS AF: 0.144

Gnomad FIN AF: 0.239

Gnomad MID AF: 0.282

Gnomad NFE AF: 0.155

Gnomad OTH AF: 0.196

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

GnomAD4 genome AF: 0.186 AC: 28201 AN: 151888 Hom.: 2709 Cov.: 31 AF XY: 0.189 AC XY: 14042 AN XY: 74228

Gnomad4 AFR AF: 0.211

Gnomad4 AMR AF: 0.193

Gnomad4 ASJ AF: 0.143

Gnomad4 EAS AF: 0.297

Gnomad4 SAS AF: 0.145

Gnomad4 FIN AF: 0.239

Gnomad4 NFE AF: 0.155

Gnomad4 OTH AF: 0.196

Alfa AF: 0.175 Hom.: 416

Bravo AF: 0.183

Asia WGS AF: 0.256 AC: 889 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.1
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11695415; hg19: chr2-218138484;