rs13412666

chr2-217041056-G-Achr2-217041056-G-C

Variant summary

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

The XR_923878.3(LOC105373874):n.7369G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.484 in 151,922 control chromosomes in the GnomAD database, including 18,583 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 0.48 (18583 hom., cov: 32)
• Consequence: LOC105373874 XR_923878.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.346

Genes affected

LOC105373874 (HGNC:):

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=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.88 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105373874	XR_923878.3	n.7369G>A		non_coding_transcript_exon_variant	3/3
IGFBP-AS1	XR_001739169.1	n.11844+47038G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DIRC3-AS1	ENST00000695932.1	n.509+47038G>A		intron_variant, non_coding_transcript_variant
DIRC3-AS1	ENST00000695934.1	n.172+47038G>A		intron_variant, non_coding_transcript_variant
DIRC3-AS1	ENST00000695937.1	n.289+3776G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.484 AC: 73490 AN: 151804 Hom.: 18560 Cov.: 32

Gnomad AFR AF: 0.396

Gnomad AMI AF: 0.399

Gnomad AMR AF: 0.585

Gnomad ASJ AF: 0.461

Gnomad EAS AF: 0.901

Gnomad SAS AF: 0.490

Gnomad FIN AF: 0.476

Gnomad MID AF: 0.386

Gnomad NFE AF: 0.487

Gnomad OTH AF: 0.492

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

GnomAD4 genome AF: 0.484 AC: 73556 AN: 151922 Hom.: 18583 Cov.: 32 AF XY: 0.486 AC XY: 36068 AN XY: 74258

Gnomad4 AFR AF: 0.396

Gnomad4 AMR AF: 0.586

Gnomad4 ASJ AF: 0.461

Gnomad4 EAS AF: 0.901

Gnomad4 SAS AF: 0.490

Gnomad4 FIN AF: 0.476

Gnomad4 NFE AF: 0.487

Gnomad4 OTH AF: 0.500

Alfa AF: 0.476 Hom.: 7191

Bravo AF: 0.493

Asia WGS AF: 0.727 AC: 2526 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	0.15
Dann	Benign	0.21

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13412666; hg19: chr2-217905779;