2-217020936-C-T

Variant names:

• chr2-217020936-C-T
• rs10177578
• ENST00000695932.1:n.509+26918C>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+26918C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.718 in 151,932 control chromosomes in the GnomAD database, including 39,698 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 0.72 (39698 hom., cov: 32)
• Consequence: DIRC3-AS1 ENST00000695932.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.130

Genes affected

DIRC3-AS1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.912 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+26918C>T		intron_variant	Intron 3 of 11
DIRC3-AS1	ENST00000695934.1	n.172+26918C>T		intron_variant	Intron 3 of 8
DIRC3-AS1	ENST00000695937.1	n.222-16277C>T		intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes AF: 0.718 AC: 108945 AN: 151814 Hom.: 39647 Cov.: 32

Gnomad AFR AF: 0.825

Gnomad AMI AF: 0.609

Gnomad AMR AF: 0.733

Gnomad ASJ AF: 0.658

Gnomad EAS AF: 0.934

Gnomad SAS AF: 0.717

Gnomad FIN AF: 0.630

Gnomad MID AF: 0.704

Gnomad NFE AF: 0.651

Gnomad OTH AF: 0.697

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

GnomAD4 genome AF: 0.718 AC: 109053 AN: 151932 Hom.: 39698 Cov.: 32 AF XY: 0.716 AC XY: 53192 AN XY: 74264

Gnomad4 AFR AF: 0.825

Gnomad4 AMR AF: 0.734

Gnomad4 ASJ AF: 0.658

Gnomad4 EAS AF: 0.934

Gnomad4 SAS AF: 0.717

Gnomad4 FIN AF: 0.630

Gnomad4 NFE AF: 0.651

Gnomad4 OTH AF: 0.700

Alfa AF: 0.660 Hom.: 51712

Bravo AF: 0.735

Asia WGS AF: 0.855 AC: 2940 AN: 3442

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.77
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10177578; hg19: chr2-217885659;