rs563290

Variant names:

• chr2-21065354-G-A
• rs563290
• ENST00000821616.1:n.240-15573C>T

Your query was ambiguous. Multiple possible variants found:

• chr2-21065354-G-A
• chr2-21065354-G-C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000821616.1(ENSG00000287956):​n.240-15573C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.698 in 151,992 control chromosomes in the GnomAD database, including 40,060 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 0.70 (40060 hom., cov: 32)
• Consequence: ENSG00000287956 ENST00000821616.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.168
• Publications: 29 publications found

Genes affected

ENSG00000287956 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.971 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
ENSG00000287956	ENST00000821616.1	n.240-15573C>T		intron_variant	Intron 1 of 1
ENSG00000287956	ENST00000821617.1	n.262-7243C>T		intron_variant	Intron 1 of 2
ENSG00000287956	ENST00000821618.1	n.524+2005C>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.699 AC: 106097 AN: 151874 Hom.: 40058 Cov.: 32

Gnomad AFR AF: 0.383

Gnomad AMI AF: 0.907

Gnomad AMR AF: 0.791

Gnomad ASJ AF: 0.693

Gnomad EAS AF: 0.994

Gnomad SAS AF: 0.847

Gnomad FIN AF: 0.813

Gnomad MID AF: 0.816

Gnomad NFE AF: 0.815

Gnomad OTH AF: 0.712

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

GnomAD4 genome AF: 0.698 AC: 106131 AN: 151992 Hom.: 40060 Cov.: 32 AF XY: 0.704 AC XY: 52315 AN XY: 74306

African (AFR) AF: 0.383 AC: 15851 AN: 41432

American (AMR) AF: 0.791 AC: 12053 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.693 AC: 2400 AN: 3464

East Asian (EAS) AF: 0.994 AC: 5143 AN: 5176

South Asian (SAS) AF: 0.846 AC: 4078 AN: 4818

European-Finnish (FIN) AF: 0.813 AC: 8610 AN: 10584

Middle Eastern (MID) AF: 0.810 AC: 238 AN: 294

European-Non Finnish (NFE) AF: 0.815 AC: 55423 AN: 67964

Other (OTH) AF: 0.716 AC: 1510 AN: 2110

Alfa AF: 0.728 Hom.: 5524

Bravo AF: 0.683

Asia WGS AF: 0.894 AC: 3107 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.0
DANN	Benign	0.69
PhyloP100		-0.17

Splicing

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

Other links and lift over

dbSNP: rs563290; hg19: chr2-21288226;