rs1921987

Variant names:

• chr2-216957190-G-A
• rs1921987
• ENST00000447289.1:n.511-36768G>A

Your query was ambiguous. Multiple possible variants found:

• chr2-216957190-G-A
• chr2-216957190-G-C
• chr2-216957190-G-T

Variant summary

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

The ENST00000607591.1(DIRC3-AS1):​n.114-24781G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.313 in 151,954 control chromosomes in the GnomAD database, including 8,372 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 0.31 (8372 hom., cov: 31)
• Consequence: DIRC3-AS1 ENST00000607591.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.467

Genes affected

DIRC3-AS1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.474 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	ENST00000447289.1	n.511-36768G>A		intron_variant	Intron 3 of 3	5
DIRC3-AS1	ENST00000607591.1	n.114-24781G>A		intron_variant	Intron 1 of 2	3
DIRC3-AS1	ENST00000695932.1	n.449-36768G>A		intron_variant	Intron 2 of 11

Frequencies

GnomAD3 genomes AF: 0.313 AC: 47493 AN: 151838 Hom.: 8374 Cov.: 31

Gnomad AFR AF: 0.150

Gnomad AMI AF: 0.371

Gnomad AMR AF: 0.361

Gnomad ASJ AF: 0.345

Gnomad EAS AF: 0.233

Gnomad SAS AF: 0.490

Gnomad FIN AF: 0.374

Gnomad MID AF: 0.380

Gnomad NFE AF: 0.382

Gnomad OTH AF: 0.322

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

GnomAD4 genome AF: 0.313 AC: 47497 AN: 151954 Hom.: 8372 Cov.: 31 AF XY: 0.317 AC XY: 23562 AN XY: 74260

Gnomad4 AFR AF: 0.150

Gnomad4 AMR AF: 0.361

Gnomad4 ASJ AF: 0.345

Gnomad4 EAS AF: 0.234

Gnomad4 SAS AF: 0.490

Gnomad4 FIN AF: 0.374

Gnomad4 NFE AF: 0.382

Gnomad4 OTH AF: 0.323

Alfa AF: 0.360 Hom.: 5075

Bravo AF: 0.301

Asia WGS AF: 0.358 AC: 1243 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	4.0
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1921987; hg19: chr2-217821913;