2-21065449-A-G

Variant names:

• chr2-21065449-A-G
• rs562338
• ENST00000821616.1:n.240-15668T>C

Variant summary

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

The ENST00000821616.1(ENSG00000287956):​n.240-15668T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.704 in 152,058 control chromosomes in the GnomAD database, including 40,468 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 (40468 hom., cov: 32)
• Consequence: ENSG00000287956 ENST00000821616.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.432
• Publications: 88 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=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.971 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000821616.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000287956	ENST00000821616.1		n.240-15668T>C		intron	N/A
	ENSG00000287956	ENST00000821617.1		n.262-7338T>C		intron	N/A
	ENSG00000287956	ENST00000821618.1		n.524+1910T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.704 AC: 107036 AN: 151940 Hom.: 40467 Cov.: 32

Gnomad AFR AF: 0.404

Gnomad AMI AF: 0.907

Gnomad AMR AF: 0.792

Gnomad ASJ AF: 0.693

Gnomad EAS AF: 0.994

Gnomad SAS AF: 0.847

Gnomad FIN AF: 0.814

Gnomad MID AF: 0.816

Gnomad NFE AF: 0.815

Gnomad OTH AF: 0.715

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

GnomAD4 genome AF: 0.704 AC: 107068 AN: 152058 Hom.: 40468 Cov.: 32 AF XY: 0.711 AC XY: 52830 AN XY: 74352

African (AFR) AF: 0.403 AC: 16717 AN: 41454

American (AMR) AF: 0.792 AC: 12095 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.693 AC: 2403 AN: 3470

East Asian (EAS) AF: 0.994 AC: 5146 AN: 5178

South Asian (SAS) AF: 0.846 AC: 4075 AN: 4816

European-Finnish (FIN) AF: 0.814 AC: 8625 AN: 10590

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

European-Non Finnish (NFE) AF: 0.815 AC: 55428 AN: 67974

Other (OTH) AF: 0.718 AC: 1516 AN: 2110

Alfa AF: 0.784 Hom.: 194281

Bravo AF: 0.688

Asia WGS AF: 0.893 AC: 3105 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.47
DANN	Benign	0.66
PhyloP100		-0.43

Splicing

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

Other links and lift over

dbSNP: rs562338; hg19: chr2-21288321;