rs10169372

Positions:

• chr2-217006626-A-G
• chr2-217006626-A-T

Variant summary

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

The ENST00000695932.1(DIRC3-AS1):​n.509+12608A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0766 in 152,102 control chromosomes in the GnomAD database, including 1,218 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 0.077 (1218 hom., cov: 32)
• Consequence: DIRC3-AS1 ENST00000695932.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.762

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 (AFR) allele frequency at 95% confidence interval = 0.236 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+12608A>G		intron_variant	Intron 3 of 11
DIRC3-AS1	ENST00000695934.1	n.172+12608A>G		intron_variant	Intron 3 of 8
DIRC3-AS1	ENST00000695937.1	n.221+12608A>G		intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes AF: 0.0764 AC: 11619 AN: 151984 Hom.: 1216 Cov.: 32

Gnomad AFR AF: 0.240

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0341

Gnomad ASJ AF: 0.0303

Gnomad EAS AF: 0.0386

Gnomad SAS AF: 0.0510

Gnomad FIN AF: 0.00151

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.00694

Gnomad OTH AF: 0.0586

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

GnomAD4 genome AF: 0.0766 AC: 11650 AN: 152102 Hom.: 1218 Cov.: 32 AF XY: 0.0744 AC XY: 5529 AN XY: 74354

Gnomad4 AFR AF: 0.240

Gnomad4 AMR AF: 0.0340

Gnomad4 ASJ AF: 0.0303

Gnomad4 EAS AF: 0.0383

Gnomad4 SAS AF: 0.0507

Gnomad4 FIN AF: 0.00151

Gnomad4 NFE AF: 0.00694

Gnomad4 OTH AF: 0.0570

Alfa AF: 0.0285 Hom.: 116

Bravo AF: 0.0859

Asia WGS AF: 0.0510 AC: 178 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	4.2
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10169372; hg19: chr2-217871349;