ENST00000695932.1:n.509+65653G>A

Variant names:

• chr2-217059671-G-A
• rs13000023
• ENST00000695932.1:n.509+65653G>A

Variant summary

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

The ENST00000695932.1(DIRC3-AS1):​n.509+65653G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.191 in 152,150 control chromosomes in the GnomAD database, including 2,987 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 (2987 hom., cov: 32)
• Consequence: DIRC3-AS1 ENST00000695932.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.563

Genes affected

DIRC3-AS1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.229 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+65653G>A		intron_variant	Intron 3 of 11
DIRC3-AS1	ENST00000695934.1	n.172+65653G>A		intron_variant	Intron 3 of 8

Frequencies

GnomAD3 genomes AF: 0.191 AC: 29043 AN: 152032 Hom.: 2978 Cov.: 32

Gnomad AFR AF: 0.151

Gnomad AMI AF: 0.202

Gnomad AMR AF: 0.183

Gnomad ASJ AF: 0.255

Gnomad EAS AF: 0.0829

Gnomad SAS AF: 0.174

Gnomad FIN AF: 0.135

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.232

Gnomad OTH AF: 0.202

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

GnomAD4 genome AF: 0.191 AC: 29063 AN: 152150 Hom.: 2987 Cov.: 32 AF XY: 0.185 AC XY: 13772 AN XY: 74370

Gnomad4 AFR AF: 0.150

Gnomad4 AMR AF: 0.183

Gnomad4 ASJ AF: 0.255

Gnomad4 EAS AF: 0.0829

Gnomad4 SAS AF: 0.175

Gnomad4 FIN AF: 0.135

Gnomad4 NFE AF: 0.232

Gnomad4 OTH AF: 0.207

Alfa AF: 0.207 Hom.: 1210

Bravo AF: 0.191

Asia WGS AF: 0.136 AC: 474 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.50
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13000023; hg19: chr2-217924394;