rs10173363

Variant names:

• chr2-217119937-G-A
• rs10173363
• ENST00000695932.1:n.509+125919G>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+125919G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.243 in 151,956 control chromosomes in the GnomAD database, including 10,054 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 0.24 (10054 hom., cov: 32)
• Consequence: DIRC3-AS1 ENST00000695932.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0390

Genes affected

DIRC3-AS1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.662 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+125919G>A		intron_variant	Intron 3 of 11
DIRC3-AS1	ENST00000695934.1	n.173-33474G>A		intron_variant	Intron 3 of 8

Frequencies

GnomAD3 genomes AF: 0.243 AC: 36890 AN: 151838 Hom.: 10017 Cov.: 32

Gnomad AFR AF: 0.668

Gnomad AMI AF: 0.0132

Gnomad AMR AF: 0.209

Gnomad ASJ AF: 0.0931

Gnomad EAS AF: 0.271

Gnomad SAS AF: 0.140

Gnomad FIN AF: 0.0107

Gnomad MID AF: 0.121

Gnomad NFE AF: 0.0464

Gnomad OTH AF: 0.202

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

GnomAD4 genome AF: 0.243 AC: 36992 AN: 151956 Hom.: 10054 Cov.: 32 AF XY: 0.240 AC XY: 17859 AN XY: 74288

Gnomad4 AFR AF: 0.668

Gnomad4 AMR AF: 0.209

Gnomad4 ASJ AF: 0.0931

Gnomad4 EAS AF: 0.271

Gnomad4 SAS AF: 0.141

Gnomad4 FIN AF: 0.0107

Gnomad4 NFE AF: 0.0464

Gnomad4 OTH AF: 0.201

Alfa AF: 0.0744 Hom.: 1695

Bravo AF: 0.277

Asia WGS AF: 0.221 AC: 769 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	2.0
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10173363; hg19: chr2-217984660;