rs2889921

Variant names:

• chr1-222166296-G-A
• rs2889921
• ENST00000416510.1:n.278+52083C>T

Variant summary

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

The ENST00000416510.1(ENSG00000236230):​n.278+52083C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.377 in 151,850 control chromosomes in the GnomAD database, including 11,550 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 0.38 (11550 hom., cov: 30)
• Consequence: ENSG00000236230 ENST00000416510.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.165

Genes affected

ENSG00000236230 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.761 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
ENSG00000236230	ENST00000416510.1	n.278+52083C>T		intron_variant	Intron 3 of 3	1
ENSG00000236230	ENST00000652067.1	n.514+22336C>T		intron_variant	Intron 4 of 6

Frequencies

GnomAD3 genomes AF: 0.377 AC: 57208 AN: 151732 Hom.: 11530 Cov.: 30

Gnomad AFR AF: 0.410

Gnomad AMI AF: 0.237

Gnomad AMR AF: 0.497

Gnomad ASJ AF: 0.314

Gnomad EAS AF: 0.780

Gnomad SAS AF: 0.355

Gnomad FIN AF: 0.404

Gnomad MID AF: 0.436

Gnomad NFE AF: 0.302

Gnomad OTH AF: 0.379

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

GnomAD4 genome AF: 0.377 AC: 57270 AN: 151850 Hom.: 11550 Cov.: 30 AF XY: 0.387 AC XY: 28733 AN XY: 74192

Gnomad4 AFR AF: 0.410

Gnomad4 AMR AF: 0.497

Gnomad4 ASJ AF: 0.314

Gnomad4 EAS AF: 0.781

Gnomad4 SAS AF: 0.355

Gnomad4 FIN AF: 0.404

Gnomad4 NFE AF: 0.302

Gnomad4 OTH AF: 0.382

Alfa AF: 0.342 Hom.: 1547

Bravo AF: 0.392

Asia WGS AF: 0.561 AC: 1949 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	3.0
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2889921; hg19: chr1-222339638;