rs1921987

Positions:

• 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 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: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.467

Genes affected

(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/exons	MANE	Protein	UniProt
		n.216957190G>A		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DIRC3-AS1	ENST00000447289.1	n.511-36768G>A		intron_variant		5
DIRC3-AS1	ENST00000607591.1	n.114-24781G>A		intron_variant		3
DIRC3-AS1	ENST00000695932.1	n.449-36768G>A		intron_variant

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;